Drupal Commons update is having troubles using drush
Drush just wasn't cut out to automatically update profiles.  pm-updatecode does not do the right thing, and as you noted, even pm-download picks the wrong location by default.


To download a new version of a module that is in a profile, use --destination to tell Drush exactly where to put the module.
If you get into a situation where Drupal no longer has the right location for your modules, run the registry rebuild tool to fix things up.