Transparency on models is very tricky.
1. the dds has to be saved in a certain compression format, I think it's DXT5
2. the transparency in the fpe needs to be either 3 or 5 (I forget which)
3. you need to set the ocluder and ocludee settings to no in the entity properties
Sometimes the modelling process itself can effect this too, sometimes you need to make the face that is to be glass last, so basically build the model, then build the glass bit.
Sometimes it just doesn't work so it's best to have the glass as a separate model.
i5, NV960 2GB, 16GB memory, 2x 2TB Hybrid, Win10.