Model not recompiling correctly?

I am using an overwatch d.va model as a skin for my TTT server; however, the eyes are very messed up. In order to see them, you have to crouch and move slightly left (your right) to see the pupils. Upon investigating this, I discovered an oddity with hlmv. When I open the original model, it works fine - eyes are correct, and body proportions are fine. However, when I decompile and recompile the model -

well, see for yourself (original on the left, recompiled on right):

and the physics model (note that they’re swapped from the last image):

additionally, a slightly edited variation (where I literally just added in a qci file with fixed hitboxes) appears invisible to everyone without the original.

It’s invisibility implies that my compiler is broken - however, the eye issue reeks of the original model having a streched pelvis/lower spine, as the eyes mimic that form. I’m really not sure, and I need help to get this up and working properly.