I'm actually curious how you got 640x480 to work at all - I am running the exact same monitor (25" Neo Geo cab), a GeForce 6200, and when I try to use QuickRes to switch to 640x480, I get a split picture. I think that means that the monitor is still getting a 31Khz signal, or something else is wrong (the video card not supporting interlaced resolutions, perhaps?). I'm running the latest ForceWare, and I'm running just the 15Khz section of soft-15khz.
Your monitor is the same as mine - it might be fuzzy because you're seeing the effects of interlacing. In the 3 different video cards that I've tried (all low end GeForce - 3, 4MX, 6200), 640x240 is the best "native" resolution that I've been able to run. My experience has been that any resolution running at 50hz rolls so bad that I can't correct it with VHold. I have been able to run some resolutions that are higher than 240 (Mortal Kombat I & II, and NBA Jam), but there is a bright area at the bottom of the screen, because the rows of pixels look like they're "rolling over" each other. I'm still trying to get Ms Pac Man (288) to run correctly, best I've been able to do is cut off the bottom.
So, what I've done is log in to the system remotely, configure MAME32 general settings, allowing the resolution to switch automatically when needed, etc and taken care of other desktop settings (lowering font size, putting the start menu on the TOP of the screen), and then coming back to the arcade cab.
Since you have a set up that is so freaking close to mine, I'd love it if we could try to figure these things out together, because some things are driving me crazy. I completely GAVE UP on MameWAH, and MAME32's option to "allow game selection with a joystick" doesn't seem to actually allow that. Basically, I need some button mapped to ESC and Enter, and I'd be fine.
My complete set up:
Pentium 2.4, 1GB RAM, Windows Server 2003 (seems odd, but it's just Windows XP, all the drivers are the same... it's my "home server")
Neo Geo cab, JAMMA harness, 25" Wells Gardner 25K7193
GeForce 6200, PCI (also have AGP GeForce 3 avail - I really want an ATI card tho)
Soft 15Khz, MAME32