I fixed more than 3000 files without problems (took 24 min, I don't know how cl*m*me perform... anyone ?)
I know. Fixing 3007 Files with clrmamepro (unzipped ROMs -> zipped MAME-ROM-Sets in another Folder) takes 2 Minutes and 53 Seconds.
http://home.arcor.de/q-marine/diverses/clrmame3007.jpg