Mesh not moving correctly with rig

I’m trying to port The Riddler from Arkham City to Garry’s mod, and to do so I copied a male armature from Half Life 2 and parented The Riddler model to it with automatic weights. I then went into Edit Mode and spent a long time assigning vertices to the armature (not many, as I was just testing) to make the rig more accurate, but when I went into Pose Mode with the armature selected, the bones would not move correctly with the mesh. I then parented a collision mesh to the armature (as this was required), and that worked fine.
I’m confused why The Riddler won’t move in time, as I remember trying Automatic Weights again with the same results.

Here is the file I’m having trouble with.

Downloaded your file…
Looked at your Rigg…
Not sure where you got this Rigg at but this is not a Rigg that will work with what your wanting to do…

this Rigg has all it’s bones… squished down into the Joints…
I can’t even begin to imagine why you would want a Rigg to be setup like that…

I suggest you use a different Rigg…

there are many very well done tutorials on how to set up a Rigg…
My suggestion is that you start with one of those and go from there…

Well, I have no idea how Valve does rigging, cause this is one of their rigs, is there any operation to remove/fix squashed joints?

Well, I have no idea how Valve does rigs, cause that was one of their male rigs. I don’t really want to set up a rig from scratch again, cause I had to move the legs, arms, and every single fingertip last time I tried a different rig. Besides, a normal Blender rig may not be compatible with Source. Is there any operation that can remove/stretch squashed joints?