I've been occasionally trying clrmame in Crossover for the last several releases, and I've been getting a crash when completing a scan. For me, the issue does not appear to be related to if the file is unzipped or zipped.
The crash does appear to be related to specific files though. To test, I tried a few files at a time, both zipped and not zipped), and it seemed to be okay for the one or two that I tested. I tried adding more files to my ROMs folder, and got a crash.
Trying to narrow it down, I tried 100 files, which caused a crash. I then tried deleting the last 50 files in that folder, and testing only the first 50, and got a crash again. HOWEVER, I then tried deleting the first 50 files, and scanning the second 50 files, and the scan completed fine.
So to me, that would indicate there is something wrong with one of those first 50 files. Not sure what that would be though, and not sure I can narrow down which of those 50 files is giving me the issue.
EDIT: just adding: I took the 100 zips I was testing, and unzipped them, and tried a scan, and that also did not crash! I then checked permissions on all of the files, and noticed most had read/write/execute permissions for user/group/public, but not all. I changed the permissions so they were read/write/execute for all individual files, and then rezipped, and again: no crash.