Good question, in fact that helped out a lot. Romlister lists "4,997" roms, my rom folder has "3,354" roms. So my issue seems to be that romlister is listing roms that I don't have the files for.
hehe, despite the absuridty of the name of the program in this situation, romlister does not actually create lists based on the roms you have.
romlister takes the XML file, that your version of MAME generates, and then makes lists based off that data. At no time does romlister actually look at what roms you have sitting on your hard drive.*
The reason why RL was written this way was twofold:
1) I didn't want romlister actually touching your roms. there are plenty of programs for that, like cmpro, romcenter, etc.
2) most people start with a fullset of roms when they figure out what MAME is all about and then go nuts over it and then decide to build a cabinet.
It is up to you to make sure that your roms folder actually has the roms that you're trying to play. Doing so is fairly easy. Either get a fullset of roms and then move over the roms that work for your machine, OR, export a list out as a "rom names" list. That will be a handy text file of the actual filename you are in need of (BIOSes not included). You can then find a fullset and select to only download those rom filenames you need.
* the above statement is completely untrue, but I didn't want to complicate the discussion.
There is a rom scan utility in the settings+tools menu. what it does is takes the MAME xml file and then parses it down to match only the available roms you have in your specified folder. This is an incredibly slow operation, and IMO, a backwards way to make your lists, so I don't recommend it.