I just ran an Audit under MAME32UI .129u5 and got this back.
Correct 7664
Incorrect 139
Total 7803
Does that mean I'm missing 139 extra files?...
Not quite. 139 of the zip files (aka rom sets) are incomplete or non-existant.
If you're missing a rom set, say a game just added in 0.129u5 and you have a complete 0.129u3 set of rom sets, and assuming the rom set has multiple roms inside, then you're missing multiple roms for that one zip file.
OTOH, if you have an incomplete rom set, say a game that got redumped for 0.129u5 and added two new previously undumped roms and you have 0.129u3 roms, then you're only part of the zip file.