lettuce, you're mixing up scan rate and refresh. Khz is the former, Hz is the latter. Anyways, yeah, this is the problem with later Mame and running native. Most games I don't have issues with; it's usually vertical games displayed horizontally, in which case I've needed to find a special mode that isn't at 15khz (refresh is more important than scan rate, you know) but most arcade multisyncs can't do this. (Presentation monitors often can, though.) Also, there may be some hardware elements, particularly in combination, involved here as these newer devices I think aren't made with such video conditions in mind.
It just came to me, though: the reason ATI's newer cards don't have the resolution restrictions Nvidia's do is perhaps due to ATI having an emphasis in display feature, whereas Nvidia's is in high-end gaming.