Drupal root getting miscalculated when sites dir is a symlink

We've been using a setup where the sites directory site side-by-side with the dir that contains core, and core/sites is a symlink to that "sibling" sites directory. This allows us to update core without danger of blowing away the sites dir; the worst that could happen is that the symlink would get deleted.

This has worked fine for drush up through version 4.5. I upgraded to 5.1 recently, though. When I ran drush from within the sites symlink and its subdirectories, I started getting these:

$ drush st
require_once(/var/www/html/d7/includes/cache.inc): failed to open stream: No such file or directory bootstrap.inc:2258                                                   [warning]
PHP Fatal error:  require_once(): Failed opening required '/var/www/html/d7/includes/cache.inc' (include_path='.:/usr/share/pear:/usr/share/php') in /var/www/html/d7/core/includes/bootstrap.inc on line 2258
Drush command terminated abnormally due to an unrecoverable error.                                                                                                       [error]
Error: require_once(): Failed opening required '/var/www/html/d7/includes/cache.inc' (include_path='.:/usr/share/pear:/usr/share/php') in
/var/www/html/d7/core/includes/bootstrap.inc, line 2258

However, running it just at the core level would work fine.

I know that there has been a fair bit of work on issues like this in the past (e.g. #648280: drush should find the drupal root correctly, even when symlinks are in use.), so for a while I assumed that the problem must have been on my side, but I've fiddled with it quite a bit and am pretty sure it's the version change. For now, I've just downgraded, but if there's anything else you think I should do in order to make 5.1 work with this situation, I'm all ears. Thanks for any suggestions you've got!