I once had all sorts of problems like that, and they're not all sorted.
BUT I found that changing the material in your script makes things
more controllable. The engine apparently assigns built-in materials
to objects itself and in my experience they are sometimes bad choices.

Create a new material in your script and turn the one in your MDL file off
and see if that helps. It did for me, Im just not sure why as I am
as still a A7 noob myself.

Hope this info is of help.