I have been running this setup for a while now with HFEA. I call the nastran.exe directly. I think I have found the issue. When I pre-process the FEM, the _i00.pm1 file changes two of the material id's without changing the material id in the properties. The _i02.f06 does give a message, but it is this:
"USER FATAL MESSAGE 311 (IFPDRV)
NON-UNIQUE FIELD 2 ON BULK DATA ENTRY MAT1 220 SORTED ENTRY COUNT = 18117
User information:
Sorted Bulk Data entry type indicated must have a unique integer
in field 2. An error in the input has been detected. Two or more
grid points, elements, or properties have the same id. (For example,
you may not use two GRID entries with the GID=2 in the same run.)"
I am working on resetting the materials in FEMAP, and see if that fixes the material re-designation during pre-processing.