Random indeed sounds weird.
I can tell you what I did for testing:
- clean cmpro installation (4.044 is current

)
- added a profile "mame 0.238" based on official mame.exe, imported the data with all SL enabled, all prompts answered with OK/YES
- quit cmpro, generated all your "O:" paths, replaced cmpro.ini and mame 0.238.cmp with your files
- put your provided aceoface zip (which actually includes all a7800 and cpc_flop versions) in your rebuilder source folder
- ran cmpro again, did a scan...everything was missing...well...sounds good
- ran a rebuilt
- ran a scan again, nothing is unneeded and the rebuilt files were ok (cpc in the cpc folder, a7800 ones in the a7800 path)
Did that several times....it is always ok...
Maybe you can setup such a clean install, separated scenario, too....maybe on a different drive...that "random" thing sounds really a bit like something is weird...maybe just bad cache data...