Try deleting your .user and .suo files – these are the user options files that VS creates. You get a .user file for each project and a .suo file for your solution. When they get corrupted, odd things happen. Deleting them will make you lose little things like which project is selected as the startup project when you start debugging, but it usually clears up odd behavior like this.
You may also want to clear out any temporary file locations, like the Temporary ASP.NET Files folders (if you’re working in ASP.NET) just in case something odd is being cached somewhere.