Ok, test one, (using the Studiomdl.exe from SFM), I removed the $Definebone statements and compiled your SMDs and got this in SFM.

https://i.imgur.com/8KlrQxi.png

https://i.imgur.com/t05u7sK.png

https://i.imgur.com/Vlzy4f0.png

Everything looks fine in SFM (unless I'm missing something). I'll compile for GMod a little later as I have to go out right now.

The model appears to be weight painted properly, however (just an observation) you do have some weirdness happening on what looks to be 4 - 8 verts painted to the window and root bone that extrudes something from behind and above the seat. If these are supposed to be rods of some kind then you have to paint them better to get the proper effect .

https://i.imgur.com/WnAN0kD.png

https://i.imgur.com/wNS308r.png

One other thing I did notice is that your Physics mesh (the collision model) is only painted to the root bone, I think the Window and the support collisions need to be painted to the proper bones.. (especially for GMod) ??

https://i.imgur.com/afxNrf5.png

Let me compile this a couple of different ways and see if I'm seeing this twisted bone problem. I may ask for the compiled model your' having problems with if I can't reproduce the problem.

I'm assuming from your picture you are compiling for SFM and or Garry's Mod??

I would have to actually examine it to give any further advice.

Vertex groups should have the same names of the bones that are deforming the mesh that is weight painted to them. If they didn't, then the model would not move.

Looks like you're exporting DMX files (I'm assuming).

If your Mesh object has the same name as the bone that controls it, the model is going to pooch out and the mesh is going to be extruded and rotated differently than it looks in Blender when compiled, This is some sort of bug (not sure if it's within the export of the DMX or the actual Studiomdl compiler screwing up.)

For example. https://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=1959841658

See how the face of this character is pulled away from the model in that picture. That is because the mesh object that was exported was named head (it created a DMX file called head.DMX) and the bone that it was weight painted to was also named head.

Check your model in Blender and see if this is the case for you. The easy fix is to start using prefixes on your bone names like bip_ or twst_ or hlp_ or def_ or att_ or weyw_
(In my case I look at these identifying what they do, like:
bip = bone in place or biped bone
twst or adj = Twist or adjustment bone
hlp = helper bone
def = deform bone
att = attachment bone
weyw = whatever you want for a prefix to a bone name)

This will ensure that the mesh object and the bone names will never be the same and you won't have this problem when you export DMX files.

Expoorting as what? DMX or SMD?

Back at you...

https://i.imgur.com/aRhypyg.png

Other than the notes, I don't see anything wrong here, unless You haven't created the shapes on the model itself OR you have another DMX that you're accidentally compiling that doesn't have shapekeys in it.

Load blender and provide a screenshot showing the project and the shapekey names.

The question then becomes, do ALL the names have an underscore in the names because if they do, they become corrective shapes in a DMX export and will disappear on compile.

If exporting SMD files are you defining the flexes, flex controllers and variables in the QC? If not, they won't be written into the model.

What is the actual name of the missing shapekey in Blender?