There is a bug in the drag and drop rebuilding after a scan. I'm using the 64 bit version with Vista. After the scan, some dropped in files won't rebuild, the CRC's match but it does nothing and says they're still missing. The only way to fix it is to manually put the file into the roms dir and then when it scans, the files are no longer missing. Example files that don't work: c1 and c8 from matrimbl. Doesn't happen on all PC's afaik.

Edit: I just remembered I forgot to check if the zip in my roms dir was write-protected or not and now it's gone. So if that could stop it from working correctly then maybe that's it(?)

I never had this problem with ClrMame until the last couple of releases.