Canderis

Well, one thing that I found out for myself, was that when I'm replacing, if I leave EVERY box checked, it will fail. I only ever check the boxes of something I've changed (usually just the torso, L arm & R arm).

I've also made the mistake a couple of times that I forget to change the extension. It's been a couple of months (3?) since I've done any modding, so I'm going from memory. First I'd select the original.mdl and then it asks for the name of the new.mdl. Next I'd select the original.mdx and it asks for the name of the new one, but (I can't remember) it comes up with a .mdl extension still. If I forget to change that, then the output will be corrupt.

I don't know if that helps, since you still haven't provided enough info.