So you are saying that its the "unchecking" of the launchbox database that is the difference here? Well that makes some sort of sense. It may be simply related to naming, you say doing it either way results in zero database ID's, but one way imports more than the other. Im guessing that when you import with the database on, that some games are combined, probably due to having very very similar short names in MAME so the database is trying to match them. When as when the database isnt called on import the roms are simply added no questions asked so to speak.
@Jason Carr a fair assumption or possible reason for this "issue"?
Also i should add that this is my conclusion as you are not using the MAME fullset importer, so Launchbox is physically matching to the database rather than the MAME.xml located in the Launchbox/Metadata folder.