I tend to leave the texture applying till last - I use characterFX for animation, so I load the mesh - then load the textures and apply them to the parts in that. It is very easy for your model to make duplicate textures or loose track of them because a lot of programs loose that information when importing - CFX makes great .X files for DBPro, so that's the logical place to apply the textures for me - maybe you should consider a final texture application right before exporting to .X.
What packages are you using?
Van-B

Muhahahahaha.