Not sure what to do....I assume its because the 31khz resolutions are no longer available?
These drivers are not specific for 15 kHz, no frequency is blocked or anything.
I assumed you weren't going to touch VMMaker. It was not necessary, that's why I didn't mention it. By looking at your first log, you had already suitable resolutions to be used. For instance, 664x496 could have been converted to 31 kHz simply by using the ranges I posted, just in ume.ini.
But you went forward and modified vmmaker.ini with the presets from GM, which uses a different non-compatible format, and you probably screwed the modelines you had installed previously, as your Modeline.txt file shows.
So, either go back to your previous config in vmmaker.ini, or port the ranges properly to the vmmaker format as explained here:
http://forum.arcadecontrols.com/index.php/topic,116023.0.html