Hi, thanks for sharing this issue.
NCrunch should normally be using the project file paths to differentiate between projects, rather than their names.. for exactly the reason that the names may not be unique :)
So this is a bit of a mystery to me. You must have managed to find a hole in the logic somewhere.
Now, the tough part is that I probably won't have much luck being able to isolate this problem with just a bug report or the project files involved. I'd need to follow through every step of the analysis, workspacing and build process to find out where it's going wrong.
This means that I can solve the problem for you (and actually, would very much like to), but I'll need a code sample that can fully reproduce it. I realise that creating code samples like this takes valuable time so I will understand if you find it easier to simply rename the project to get NCrunch to work. Probably I would recommend renaming it anyway, just because it's very confusing to have two projects under the same name :)
Cheers,
Remco