I have limited knowledge, but I would start with this:
1. You verified your model works. so we will eliminate the model as a cause for now.
2. Open Cutscene Editor, take a look at the original model and compare with your replaced model by looking at the model materials.
Verify that the textures that you need, exists. Specifically look for texture names to see if both new and old models use the same texture names. If they do not, then you must manually do texture by id swaps on your new model.
If you are unfamiliar with texture swapping, refer to DrSuperEvil's and BorgDragon's thread on texture swapping by id (link is in his signature. Also, i recommend reading that thread in this order: page1-4 then start at the last page and read in reverse page order)
3. If still not working; check your model again. Look for variances in opacity texture settings and alpha texture settings. If you find variances, find someone who knows a lot about custom model making and 3rd party modeling programs.
This should give you a good starting point to narrow down the cause.