Uh not sure how but it kinda solved itself this morning when I reloaded the model and the textures. <3 random stuff! Thanks for the help though everyone!
I think the issue isn't in the UV here; so unwrapping everything again won't solve it. As toedar23 said it's probably the face normal that are probably messed up.
This is completely solved in 2020. There is a new 'mode 5' which runs in the background and significantly speeds everything up. This command panel issue was known to the devs and it's been resolved.
I would look into Maxscript to solve this. You could look at this script as an example, and expand upon it if needed. http://www.scriptspot.com/3ds-max/scripts/max-defaults
In the FFD Parameters, try changing Deform to "All Vertices". If this solves it, it's because you've started with a planar mesh, so there was zero depth on Z for the FFD volume to grab with.