Windows apps fail to launch, bottle deletion fails with lengthy error message
This is a fairly uncommon issue
If your Crossover files have had their permissions re-set with an Access Control List (ACL), Crossover won't be able to over-write the files with new contents. ACL settings can be applied in some circumstances by modifying the "Sharing and Permissions" section of a file's "Get Info" menu, and then choosing to apply those settings to a whole directory (if the directory contains Crossover files).
If this happens, Crossover will fail to launch your windows apps after your next Crossover upgrade, at which point the over-writing fails. Crossover will also be unable to delete bottles from the Manage Bottles menu. "Clear and Rebuild Programs menu" will not give you working menu items, either, however you should be able to launch apps manually using Run Command and browsing manually to the .exe of your windows app.
If you look into your Console Log, you will see errors resembling the following:
5/08/11 6:21:45 PM [0x0-0x208208].com.codeweavers.CrossOver wineserver: could not save registry branch to user.reg : Permission denied
5/08/11 6:21:45 PM [0x0-0x208208].com.codeweavers.CrossOver wineserver: could not save registry branch to system.reg : Permission denied
To fix this issue, open up a terminal (Applications>Utilities>Terminal) and enter the following commands: