We've moved from CVS to Subversion, so I wanted to remove the CVS options from the main menu. I went into Project Settings / Menus and Toolbars and deleted the CVS nodes from the Version Control menu. When I OK'd the changes and looked at the main menu, the Version Control submenu had multiple Show Coverage Data and Generate Coverage Report entries in it. I went back in to the Project Settings to clear them out, but they didn't show. I then moved the remaining Version Control entries up to fill the spaces left by deleting the CVS entries. When I returned to view the main menu, there were even more Show Coverage Data and Generate Coverage Report entries in it.
My Version Control menu now looks like this, and I can't see a way to fix it short of manually editing the configuration file:
This looks like an old bug that has come back again - I had exactly this problem a long time ago.