@oxyandy
I have installed 9.28a and set my 7z tab in compressor properties identical to yours in your pic. The problem with roms missing still can be 100% reproduced and it seems to be the exact same roms/sets everytime!
Let me explain the steps I use to reproduce this issue.
- load official MAME 147 binary into CMP
- rebuild complete 147 romset into empty destination directory with merge sets ticked and zip or 7z does not matter
- after rebuild is complete jump to scanner and audit destination directory which shows 0 misses
- right click in the profiler and delete profile + clean cache
- load self compiled 147u3 into profiler
- scanner execute scan + fix all option with you prefer merge sets
- rebuild from source MAME - Update ROMs (v0.147 to v0.147u3) with merge sets ticked
- rebuild from backupPath
result is 27 are missing so where did they go?
http://pastebin.com/mxNBmuh0