Scott, this will probably not solve your problem, but should at least explain what is happening. I'm travelling at the moment, away from my development system, and will be for the balance of the week. So, I'm "winging it" a bit.
TexturesUsed.txt is not a list of all the textures used by the model (that can be obtained by opening the .mdl file itself). Rather, it is a list of the custom textures used by the .mdl so that you will know which textures to copy if you don't let SAMM move those textures to the "final" texture folder. If the model uses textures from, say, the FSX\Textures folder, then those textures are not saved with the model since it is assumed they will be available from the main \Textures folder when the model is subsequently rendered, in your case P3D\Textures.
So, you should be checking whether the missing textures are available in the P3D textures folder.
I could, of course, have designed SAMM differently, but it didn't seem necessary at the time - on the assumption that such textures would be carried over from one version of Flightsim to the next.
If the missing textures are actually in the P3D\Textures folder, then it would seem my P3D implementation of SAMM is deficient. Unfortunately, since I don't have access to my development syste?m, I can't check. If this is the situation in your case, please post again (or e-mail me) in about a week, and include a link to the aircraft for which the difficulty exists (so that I can attempt to duplicate the exact problem you are reporting) and I'll investigate further.
On the other hand, if the problem is due to the mising texture(s) not being in your P3D\Textures folder, then this is probably a circumstance I can "fix" in SAMM. As an interim solution, try to obtain a copy of the missing texture(s) from the version of Flightsim for which the aircraft was designed and copy that/them into your P3D\Textures folder.
In any case, it will have to wait for a week or so.
Don