Hello. What I think is happening is that the game has a few different, random "appearances" for the upgraded SdKfz 251. I did a quick test with Janne's cheatmod and spawned 15 halftracks, upgraded them to flame, and 2 out the 15 had the covering all the way. The rest looked like what you've described as "broken".
It appears there's no reason or requirement why sometimes it spawns fully covered or not.
Similarly, the SdKfz 222/221 will spawn with a random look as well. Sometimes they will have a rolled up canvas with a chest on the front end, sometimes nothing, sometimes rolled up canvas on rear only, etc..
As far as your lighting question, I believe your problem is your burn settings if you are saving _nrm, _gls, and _spc separately. I personally don't export all those because the file size of the skin pack starts to get really large. I just try to adjust the _dif's coloring, lightness, etc. to compensate. I can send you my burn settings if you want to see if that works for you.