Thanks for the help. The log file is a 70K pile of mess, but I'll paste some parts I think are interesting:
advance:generate: modeline "generate 5.95782 288 320 336 384 224 237 240 256 -hsync -vsync"
advance:generate: failed to generate mode generate-interlace
advance:generate: failed to generate mode generate-double
advance:generate: failed to generate mode generate-double-interlace
advance:generate: failed to generate mode generate-triple
advance:generate: failed to generate mode generate-quad
emu:video: best mode 288x224, mode2x 576x448, mode3x 864x672, bits_per_pixel 16, vclock 60.6061
...
video: mode_set generate 288x224 bgr16 15.52/60.61
...
video:svgaline: mode_set modeline 5.95782 288 320 336 384 224 237 240 256 -hsync -vsync
video:svgaline: expected vert clock: 60.61 Hz
...
video: measured/expected vert clock: 74.99/60.61 = 1.23733 (err 23.7335%)
....
emu:video: mode generate, size 288x224, bits_per_pixel 16, bytes_per_scanline 576, pages 1
emu:video: vsync disabled because the vclock is too different 60.6061 74.99
...
emu:video: vsync disabled because fastest active
emu:video: vsync disabled because the vclock is too different 60.6061 74.99
So it's trying to run me at 75 Hz. Fabulous. You know, I had the mode SORT OF working before on the same hardware. Sort of, because instead of giving me the arcade-true refresh, it would ALWAYS spit out my MAXIMUM chosen refresh instead. And I don't think I was able to get it to 60.60606 Hz for some reason.
The card is an onboard Ati Rage of some sort. All I really want is to get Pac-man and similar games working, just for now (for christmas.) Even if I have to hard-force one single modeline, and squash all games into it for now, that would still be great for most of the Pac-mans, Galaga, Frogger, and probably others, so that would be fine. Later I want to upgrade the hardware, and even get an ArcadeVGA if I have to. For now I just want my Pac Man.
I was hoping EasyMAMECab would fix everything this time, but I am going to try putting that arcade-frequency TSR back in, and then running advcfg like I did before. But before that seemed to screw my advmenu to prevent it from working...