Updating Drupal core to 6.19 with drush up deactivates all modules

During a "drush up" to update Drupal Commons to Drupal 6.19, I get the following error message (excerpt):

Code updates will be made to drupal core.
WARNING:  Updating core will discard any modifications made to Drupal core files, most noteworthy among these are .htaccess and robots.txt.  If you have made any modifications to these files, please back them up before updating so that you can re-create your modifications in the updated version of the file.
Note: Updating core can potentially break your site. It is NOT recommended to update production sites without prior testing.
Do you really want to continue? (y/n): y
Project drupal was updated successfully. Installed version is now 6.19.
Backups were saved into the directory                                                                            [ok]
/volumes/devdisk/htdocs/drupal_commons/backup/modules/20100820140644/drupal.
<em>module</em> <em>admin_menu</em> is incompatible with this release of Drupal, and will be disabled.           [warning]
<em>module</em> <em>ajax_load</em> is incompatible with this release of Drupal, and will be disabled.            [warning]
<em>module</em> <em>better_formats</em> is incompatible with this release of Drupal, and will be disabled.       [warning]
...

These messages appear for all modules with the result that all modules are disabled and the site is effectively destroyed.

Of course I made a backup beforehand but I thought that this is an interesting behavior that should be addressed.