Hmm, I'm not sure about custom models but it's an interesting thought. I can't think of any reason why a point shop model over the default models would cause an issue. I'm not very familiar with GMODs model integration but would assume it requires custom player models to have specific things for it to function correctly with the engine. Since we don't really see any other issues with the model when people are playing I would only assume the model is ok. If there was a physics issue with it I think we would see it when someone is moving around with that model.
I would like people to test the new server I setup and see how that goes. We could just be looking at some corrupt files because of the age of the install.