> Any ideas at all as to what may have happened?
>

No...and I'm not sure if I understand you right.
You got a MAME32 installation with roms stored in rompath XYZ.
You've setup rompath XYZ in ClrMamePro->Settings->Rompaths, scanned...fixed..blablba...
After that you don't see XYZ on your harddisk anymore but MAME32 loads the files from XYZ?

...or do I miss something?

Roman Scherzer
ClrMamePro