He is right, sometimes the Resource Compiler does have either a setting or a glitch that will transform your texture into a square. I have run into that personally. But he is also wrong:
Make sure perspective is off, and perhaps limit which directions your brush pushes in (transform: modifiers). Or try a more subdivided grid with a higher wrap mode setting
On a site note, is there a valid reason why 3dsmax can't undo a reset xform? Maya has no problem undoing freeze transformation, don't really see how that's different...
If you're fill-bound, the vertex color is very attractive, since it's only a vertex shader. But if you're only transform-bound (and have RAM to spare) then IMHO lightmaps are the best.
Sounds like you need to freeze transformations, reset xform, etc. You can also utilize the 3d previewer in xNormals and check to see if you're models are overlapped.
Are the bones in the exact same world space? Maya gets confused if multiple bones shares the same world space transform since it picks the bones based on mirrored location.
Issue #2 I can't figure out how to use the "move tool" people are using to move(shape) the face of the model around for shaping ( not transforming/moving tool ).