To answer my own question:
I did indeed miss something.
Although I updated USSEP versions regularly (406+MPfix->407->408), I never really noticed my issue until recently.
It seems I missed that a texture replacer for the Apple-pie also included it's own mesh for the pie.
NMM did not warn of an 'overwrite' because the default is in a BSA.
I did not know that the Apple-pie mesh is the same as the Meat-pie mesh inserted by USSEP.
So, if you touch the Apple-pie, you lose the texture of the USSEP Meat-pie.
Case closed, & pies eaten.