He said his mvps are in his root, and his root is in the paths.
I would check that the priority you want is correct, I'd bet that it's either loading from another path first, or, PCS2 didn't follow the same priority order for going through the mediavps that FS2 would. That would probably be a bug then. But yeah, shame on you for throwing your mvps in with all your other stuff. The other possibility is that your paths didn't get saved the way you thought you typed them in, there's a couple small bugs in the preferences pane that might have caused that. But yeah, I bet it's some sort of priority issue, if everything is set up right on your end.