I use clrmamepro with merged sets (which is probably 1/2 my problem) and I have been encountering some strange problems of late. In the last month I have noticed single rom updates to sets sometimes has wierd results. More than twice now the single rom updates itself at the expense of the rest of the archive (which usually completely or partially disapears instead of moving to the back up folder - though why would it as it wasn't meant to be deleted). I know these files were there previously as I have been able to restore them from my archived backups. It only ever seems to happen to one set only in a single update and not every update.
Tonight I tried to test my new compile using Bust a Move (pbobblen). Clrmamepro reported it as complete but mame correctly advised me there were a bunch of roms missing (which I found in the pspike archive). This may be totally unrelated to the other problem but I thought you may want to know about it.
Im sorry I cant be more specific about these problems as I didn't think much of them at first. I'll definitely keep a list from now on and report anything strange I find.
Cheers
Chook.