Originally Posted by DamienD
A few reasons I can think of:
... Maybe some of the roms were bad dumps and then replaced later when a good dump has been achieved / verified. Dumping roms can be very difficult, just check out some of the information / images posted by The Guru
and you'll get a better idea of the complexity.
... The names of roms have been renamed to match schematics.
There are probably a few other possible reasons that sadly elude me at present.
As said by Damien really. If you go through CLRMAME before you update your ROMs that will fix / rename the majority it can and then get rid of the rubbish ones before it updates to the latest version. To be honest the ROMs are the least of your worries. It's the CHD's that are the killer and if they get mis-dumped and you have to donwnload them again it's a very sickening moment!