I have recently been getting an error in the Windows Forms designer of VS2010SP1 when using inherited UserControls.
The error is
The designer
I would suggest putting your base class in a separate project. As you obviously know, the problem is that VS is losing track of some meta information, which you can get it to find by quitting and rebuilding. If the base class is in a separate project, a clean/rebuild is more likely to bring it back up to date.