what is the alpha channel?
Ryan,
It's a bitmap that you add to the texture bitmap using DXTbmp. It controls the amount of shine that the aircraft has. Some aircraft don't support alpha textures as they were not added to the model when the aircraft was designed for FS. If you were to add an alpha texture to a texture for an aircraft that does not support alpha textures the aircraft would appear semi-transparent in FS.
Try loading the texture that corresponds to the part of the aircraft that is transparent and see if it has an alpha channel.
Regards,
Stratobat