I was having this problem also, as well as seemingly related crashes when doing a complete build on a project after it was pushed to my plastic cloud repo.
I was able to fix it by not using Unity's Resource Loader. So I renamed the Resources folder to something else like MyResources, which stopped Unity from packing that folder for use by the Resources.Loader. Then I changed my code to load things from scene objects or prefabs. And it all started working.
I have since been putting a few things back into the Resources folder only when necessary and it is still working.
So I believe that some file comes back from Plastic SCM with something in it, probably in its meta data, that trips up Unity. I am not 100% sure, but I would try renaming your Resources folder and see if it fixes the problem.