It may not even be related to Visual Studio 2010, I've seen Windows Installer sometimes get stubborn and ask for old installation files from something you removed or attempted to remove before. It's almost like it has a list of unfinished business and tries to finish it when invoked. You could start with reinstalling VS 2010 and your updates, I'd be curious to see if the Event Viewer could shed some more light on the issue, is it logging anything when this happens?
As much as I hate "Registry Cleaners" there is
one by Auslogics that has never steered me wrong or hindered a system with negative effects, and I'm pretty sure it checks Windows Installer locations and repairs errors if found, you may create a System Restore point...