Ok, I had to move the vms pk3 completely out of the tremulous basepath to get it to look at my qvms. Once I do that I get an error saying that it can't load ui.qvm. Files in the cgame directory shouldn't effect that right? So I grab the original ui.qvm from the original vms.pk3 and try that, which fails in the same way. Also, its trying to find a file called mod.cfg.
I'm going to mess around with this some more and see if I can get rid of this error