FSX is slightly different to previous versions in that it will "guess" textures if the coded one is missing. eg if the model calls for xyz.bmp and it can`t find it it will look for xyz.dds and try that. Can get confusing
It also seems to handle the alpha channels slightly differently and use much higher transparency when FS9 models/textures are used in FSX

Try converting some to DDS (may need flipping if they appear upside down on the model) and try lightening the alpha channel if still coming up transparent