I'm using the release of .145. I'm pulling the dat info from MameUI64.exe.
Yes, I have clrmamepro set for split sets. I haven't changed anything since running a successful scan with 4.02. When I saw you released an update, I installed it and ran the scanner again just to verify that I had everything cleaned up. There were actually about 15 empty folders that were in my chd folder that disappeared. I recreated the folders two at a time and then re-ran a scan. They were removed from the scan results. When I got to the two code1d(b) folders, I created them, re-ran the scan, and they were deleted.
I've gone into Profiler and cleared the cache. After rebuilding the datfile, I still get the same results. It just these two folders that are not playing nicely. If you need me to post/send anything, let me know. It's not a HUGE deal, but it is a little annoyance that I can't seem to figure out.