Thanks, it never hurts to check the simple stuff first, right? Otherwise, I might be chasing another rabbit which I tend to do sometimes from poor reading comprehension.
Anyway, I take it you're using AM to generate the romlist, right? And, there is nothing wrong with that method. But, have you tried importing your list from the cmd line? Say, with something like the hyperspin databases (emulator.xml) for example. With AM, you can import xmls on the command line with relative ease. And, the good thing about using the XML databases is they are usually updated for you. I use them myself, all my romlist for AM are generated by using xml DB files.
If you want to give it a try, just grab whatever emulator.xml you want to use and drop it into your AM root folder. Then drop to the cmd line, and type attract -i mame.xml mame. The latter is the name of the emulator which should be setup prior to running this command. This whole process only takes a few seconds.