I just went through every texture in this plane, and made them all transparent, then went through and colored every part a different color, and the only thing that did not change each time is that VC texture. :-/
I am now convinced that this is part of the model that is just interpreted differently by different systems.
There are no textures in any of the texture folders that affect the VC canopy, if there were, I would surely have found it through this method.
On a lighter note, it was really funny flying around in an invisible airplane with a blacked out canopy.

The only way I see this able to be fixed is getting the original source files and adjusting the VC canopy that way. I have sent multiple emails to the KBT website and have never heard anything back.