I have seen this once with Office references in VS2012.
I think for some reason the change is not persisted back to the project file. And the compiler uses the file, which is reloaded when you check the references
The answer was to right click -> unload the project, then right-click again and edit the project file. By manual inspection, make sure the references are OK. Then just save the file and you should be good to go.
This bug in VS has been corrected now