It might not be updating the references if you haven't checked out/checked in the assemblies. In other words the where used might not be updated until doing so.
See what happens if you open up an assembly and check it out using "get latest".
I don't know in PDM Standard if you can paste as reference into other folders, but you might want to look into that. Personally I don't like it, but to each their own.
I tried that but no success.