Missing sets: Well, there are some sample-only and some chd-only sets in MAME. If you don't have the belonging samples/chds, the set is missing, no matter if you disabled scanning chds/samples. The reason is simple, a set is a collection of roms and/or samples and/or chds. So if you scan for sets, you scan for the existance of sets, the right name if they are needed or not. If you're additionally scanning for chds/roms/samples, you also scan the set containers themeelves, so e.g. the correct checksum of a romfile, the name or sha1 of a chd file, etc..
So if you're scanning for sets without having all chds (or samples), you will end with missing sets, due to the fact that there are some sets which only consist of a chd/sample.
Fixed romnames, if you only d a scan without enabling the fix options, you see what is wrong (well, since it's now too late anyway, don't really worry about it). Hard to say what was actually wrong before. It is pretty common that romnames change from mame version A to B. 6081 sounds a lot, but if some commonly used files are renamed the number grows quickly.
Stats don't really matter at all....if your scan results tree window is empty, you're done.
Rollbacks: let's start the other way around, newer MAME versions replace bad dumps, resize overdumps, rename sets, reorder parent/clone relationsships, add a bunch of new stuff etc etc...So some files are simply not needed anymore. So if you're doing a rollback, you need to find these old bad stuff again. The rebuilder is a pretty straight forward test-checksum-and-recreate-file maching. If it finds a valid file in the source, it adds it to the destination. It's not setbased but file based, so it's not its purpose to create fully sets.
If your rebuilt rollback sets are incomplete you simply miss the belonging file. Maybe you got it in your cmpro backup folder, maybe you never had it.
And don't forget between 164 and 106 there are 58 (!!!) versions in between. I don't know how rollback sets are organized but maybe you need all rollback sets in between, too........actually there is no real reason to rollback anyway ;-) but that's a different story.