Smith Micro would no doubt tell you that MAT poses are not a supported feature, and never have been, despite e-frontier distributing some with Poser 5. ;) It's not impossible that a MAT pose is unable to properly 'root out' some node structure that was present in the previous material, and in that case starting from scratch is the simplest work-around. That combination wouldn't have been tested for, anyway.

I do occasionally find hiccups with MAT poses myself. Sometimes, applying them while you're in the material room seems to make things work better, but I haven't tested the phenomenon thoroughly.