Well, I'd still flush everything - the bin and obj folders from your projects. We often set up "flush" bat files for this purpose - both to clean to avoid odd problems like this, and to reduce the zip size should we send the solution to anyone. After flushing, back in Visual Studio do a rebuild.
It's possible that the project dependencies defined for the solution aren't correct somehow too, so that might be worth checking.
If you place any of your assemblies in the GAC, then that could be causing the problem if an older assembly with matching major/minor version is found.
Visual Studio will also cache assemblies for designer purposes. You can also try clearing the C:\Users\<user>\AppData\Local\Microsoft\VisualStudio\10.0\ProjectAssemblies folder.