drush update taxonomy_manager deletes sites directory

drush updates all of my other modules correctly. But when I have it upgrade taxonomy_manager, I get the following errors, and my entire sites directory is deleted:

healingthresholds:/var/www/backup.healingthresholds.com$ drush up
Refreshing update status information ...
Done.
Update information last refreshed: Sun, 2010-02-21 00:29

Update status information on all installed and enabled Drupal modules:
 Name                         Installed       Proposed        Status     
                              version         version                    
 Advertisement                6.x-2.2         6.x-2.2         Up to date 
 Ad GeoIP                     6.x-2.0-rc1     6.x-2.0-rc1     Up to date 
 Administration menu          6.x-1.5         6.x-1.5         Up to date 
 lm_paypal                    6.x-1.0         6.x-1.0         Up to date 
 Backup and Migrate           6.x-2.2         6.x-2.2         Up to date 
 Backup and Migrate Files     6.x-1.x-dev     6.x-1.x-dev     Up to date 
 Bibliography Module          6.x-1.10        6.x-1.10        Up to date 
 Drupal                       6.15            6.15            Up to date 
 Boost                        6.x-1.18        6.x-1.18        Up to date 
 Content Construction Kit     6.x-2.6         6.x-2.6         Up to date 
 (CCK)                                                                   
 Chaos tool suite             6.x-1.3         6.x-1.3         Up to date 
 Email Field                  6.x-1.2         6.x-1.2         Up to date 
 Environment Indicator        6.x-1.0         6.x-1.0         Up to date 
 External Links               6.x-1.9         6.x-1.9         Up to date 
 FileField                    6.x-3.2         6.x-3.2         Up to date 
 GeoIP API                    6.x-1.x-dev     6.x-1.x-dev     Up to date 
 Global Redirect              6.x-1.2         6.x-1.2         Up to date 
 Glossary                     6.x-1.6         6.x-1.6         Up to date 
 GMap Module                  6.x-1.0         6.x-1.0         Up to date 
 Google Custom Search Engine  6.x-1.2         6.x-1.2         Up to date 
 Google Ad Manager            6.x-1.x-dev     6.x-1.0         Up to date 
 Google Analytics             6.x-2.2         6.x-2.2         Up to date 
 ImageAPI                     6.x-1.6         6.x-1.6         Up to date 
 ImageCache                   6.x-2.0-beta10  6.x-2.0-beta10  Up to date 
 ImageField                   6.x-3.2         6.x-3.2         Up to date 
 Imagefield Crop              6.x-1.0-rc1     6.x-1.0-rc1     Up to date 
 IMCE                         6.x-1.3         6.x-1.3         Up to date 
 IMCE Wysiwyg bridge          6.x-1.0         6.x-1.0         Up to date 
 jQuery plugins               6.x-1.10        6.x-1.10        Up to date 
 jQuery UI                    6.x-1.3         6.x-1.3         Up to date 
 Keys                         6.x-2.0         6.x-2.0         Up to date 
 Link                         6.x-2.8         6.x-2.8         Up to date 
 Location                     6.x-3.0         6.x-3.0         Up to date 
 LoginToboggan                6.x-1.6         6.x-1.6         Up to date 
 Term lower name              6.x-1.1         6.x-1.1         Up to date 
 Mollom                       6.x-1.12        6.x-1.12        Up to date 
 Nice Menus                   6.x-1.3         6.x-1.3         Up to date 
 Nodewords                    6.x-1.11        6.x-1.11        Up to date 
 Page Title                   6.x-2.3         6.x-2.3         Up to date 
 Panels                       6.x-3.3         6.x-3.3         Up to date 
 Path redirect                6.x-1.0-beta6   6.x-1.0-beta6   Up to date 
 Pathauto                     6.x-1.2         6.x-1.2         Up to date 
 Prepopulate                  6.x-1.1         6.x-1.1         Up to date 
 Quick Tabs                   6.x-2.0-rc4     6.x-2.0-rc4     Up to date 
 Rotor Banner                 6.x-2.4         6.x-2.4         Up to date 
 Rules                        6.x-1.1         6.x-1.1         Up to date 
 Scheduler                    6.x-1.6         6.x-1.6         Up to date 
 Search 404                   6.x-1.8         6.x-1.8         Up to date 
 Special menu items module    6.x-1.4         6.x-1.4         Up to date 
 Taxonomy Manager             6.x-2.1         6.x-2.2         Update     
                                                              available  
 Term Node Count              6.x-1.3         6.x-1.3         Up to date 
 Token                        6.x-1.12        6.x-1.12        Up to date 
 Top Searches                 6.x-1.1         6.x-1.1         Up to date 
 Upload element               6.x-1.2         6.x-1.2         Up to date 
 Views                        6.x-2.8         6.x-2.8         Up to date 
 Views Type Block             6.x-1.0         6.x-1.0         Up to date 
 Views Bulk Operations (VBO)  6.x-1.9         6.x-1.9         Up to date 
 Webform                      6.x-2.9         6.x-2.9         Up to date 
 Wysiwyg                      6.x-2.0         6.x-2.0         Up to date 
 XML sitemap                  6.x-2.0-alpha2  6.x-2.0-alpha2  Up to date 

Code updates will be made to the following projects:
Taxonomy Manager [taxonomy_manager-6.x-2.2]

Note: Updated modules can potentially break your site. It's not recommended to update production sites without prior testing.
Note: A backup of your package will be stored to backups directory if it is not managed by a supported version control system.
Note: If you have made any modifications to any file that belongs to one of these projects, you will have to migrate those modifications after updating.
Do you really want to continue? (y/n): y
Project taxonomy_manager was updated successfully. Installed version is now 6.x-2.2.
Backups were saved into the directory                                [ok]
/var/www/backup.healingthresholds.com/backup/modules/20100221052915.

Fatal error: require_once(): Failed opening required './sites/all/modules/backup_migrate/includes/crud.inc' (include_path='.:/usr/share/php:/usr/share/pear') in /var/www/backup.healingthresholds.com/sites/all/modules/backup_migrate/backup_migrate.module on line 208
Drush command could not be completed.                                [error]

Here are the results when I first disable and uninstall backup_migrate and backup_migrate_files:

healingthresholds:/var/www/backup.healingthresholds.com$ drush up
Refreshing update status information ...
Done.
Update information last refreshed: Sun, 2010-02-21 00:36

Update status information on all installed and enabled Drupal modules:
 Name                         Installed       Proposed        Status     
                              version         version                    
 Advertisement                6.x-2.2         6.x-2.2         Up to date 
 Ad GeoIP                     6.x-2.0-rc1     6.x-2.0-rc1     Up to date 
 Administration menu          6.x-1.5         6.x-1.5         Up to date 
 lm_paypal                    6.x-1.0         6.x-1.0         Up to date 
 Bibliography Module          6.x-1.10        6.x-1.10        Up to date 
 Drupal                       6.15            6.15            Up to date 
 Boost                        6.x-1.18        6.x-1.18        Up to date 
 Content Construction Kit     6.x-2.6         6.x-2.6         Up to date 
 (CCK)                                                                   
 Chaos tool suite             6.x-1.3         6.x-1.3         Up to date 
 Email Field                  6.x-1.2         6.x-1.2         Up to date 
 Environment Indicator        6.x-1.0         6.x-1.0         Up to date 
 External Links               6.x-1.9         6.x-1.9         Up to date 
 FileField                    6.x-3.2         6.x-3.2         Up to date 
 GeoIP API                    6.x-1.x-dev     6.x-1.x-dev     Up to date 
 Global Redirect              6.x-1.2         6.x-1.2         Up to date 
 Glossary                     6.x-1.6         6.x-1.6         Up to date 
 GMap Module                  6.x-1.0         6.x-1.0         Up to date 
 Google Custom Search Engine  6.x-1.2         6.x-1.2         Up to date 
 Google Ad Manager            6.x-1.x-dev     6.x-1.0         Up to date 
 Google Analytics             6.x-2.2         6.x-2.2         Up to date 
 ImageAPI                     6.x-1.6         6.x-1.6         Up to date 
 ImageCache                   6.x-2.0-beta10  6.x-2.0-beta10  Up to date 
 ImageField                   6.x-3.2         6.x-3.2         Up to date 
 Imagefield Crop              6.x-1.0-rc1     6.x-1.0-rc1     Up to date 
 IMCE                         6.x-1.3         6.x-1.3         Up to date 
 IMCE Wysiwyg bridge          6.x-1.0         6.x-1.0         Up to date 
 jQuery plugins               6.x-1.10        6.x-1.10        Up to date 
 jQuery UI                    6.x-1.3         6.x-1.3         Up to date 
 Keys                         6.x-2.0         6.x-2.0         Up to date 
 Link                         6.x-2.8         6.x-2.8         Up to date 
 Location                     6.x-3.0         6.x-3.0         Up to date 
 LoginToboggan                6.x-1.6         6.x-1.6         Up to date 
 Term lower name              6.x-1.1         6.x-1.1         Up to date 
 Mollom                       6.x-1.12        6.x-1.12        Up to date 
 Nice Menus                   6.x-1.3         6.x-1.3         Up to date 
 Nodewords                    6.x-1.11        6.x-1.11        Up to date 
 Page Title                   6.x-2.3         6.x-2.3         Up to date 
 Panels                       6.x-3.3         6.x-3.3         Up to date 
 Path redirect                6.x-1.0-beta6   6.x-1.0-beta6   Up to date 
 Pathauto                     6.x-1.2         6.x-1.2         Up to date 
 Prepopulate                  6.x-1.1         6.x-1.1         Up to date 
 Quick Tabs                   6.x-2.0-rc4     6.x-2.0-rc4     Up to date 
 Rotor Banner                 6.x-2.4         6.x-2.4         Up to date 
 Rules                        6.x-1.1         6.x-1.1         Up to date 
 Scheduler                    6.x-1.6         6.x-1.6         Up to date 
 Search 404                   6.x-1.8         6.x-1.8         Up to date 
 Special menu items module    6.x-1.4         6.x-1.4         Up to date 
 Taxonomy Manager             6.x-2.1         6.x-2.2         Update     
                                                              available  
 Term Node Count              6.x-1.3         6.x-1.3         Up to date 
 Token                        6.x-1.12        6.x-1.12        Up to date 
 Top Searches                 6.x-1.1         6.x-1.1         Up to date 
 Upload element               6.x-1.2         6.x-1.2         Up to date 
 Views                        6.x-2.8         6.x-2.8         Up to date 
 Views Type Block             6.x-1.0         6.x-1.0         Up to date 
 Views Bulk Operations (VBO)  6.x-1.9         6.x-1.9         Up to date 
 Webform                      6.x-2.9         6.x-2.9         Up to date 
 Wysiwyg                      6.x-2.0         6.x-2.0         Up to date 
 XML sitemap                  6.x-2.0-alpha2  6.x-2.0-alpha2  Up to date 

Code updates will be made to the following projects:
Taxonomy Manager [taxonomy_manager-6.x-2.2]

Note: Updated modules can potentially break your site. It's not recommended to update production sites without prior testing.
Note: A backup of your package will be stored to backups directory if it is not managed by a supported version control system.
Note: If you have made any modifications to any file that belongs to one of these projects, you will have to migrate those modifications after updating.
Do you really want to continue? (y/n): y
Project taxonomy_manager was updated successfully. Installed version is now 6.x-2.2.
Backups were saved into the directory                                [ok]
/var/www/backup.healingthresholds.com/backup/modules/20100221053626.

Fatal error: require_once(): Failed opening required './sites/all/modules/panels/includes/plugins.inc' (include_path='.:/usr/share/php:/usr/share/pear') in /var/www/backup.healingthresholds.com/sites/all/modules/panels/panels.module on line 285
Drush command could not be completed.                                [error]

Instead, I disabled, uninstalled, and deleted taxonomy_manager, did the upgrade, and then reinstalled taxonomy_manager using drush. This worked fine.