Once the PC is shutdown it should remember to use 640x480 on the next start up. Mala has an option to Start up with Windows. So I just need to find a way to boot my PC with the Arcade Monitor hooked up without ruining it.
I believe it is physically impossible to get the BIOS screens of a PC to boot in a non-31Khz without additional hardware. Likewise with Windows XP, you can't set the default loading screens resolution that I am aware of.
Only options:
1) Jpac/AVGA - you don't want to.
2) build a circuit that will only pass ~15Khz signals, and block 31Khz signals. This would work, not damaging your monitor, but you would see nothing until XP had booted and changed to your 15Khz signal.
3) Ditch XP, and use linux as I believe you can set the framebuffer from boot to be 15Khz (I don't know how, but have read about it). This would leave the bios - but you could investigate LinuxBios project, where you flash you motherboards bios with some linux bootcode. Not easy,straightforward or likely to work IMHO.
4) Probably your best option - add a second VGA card. You can often set which VGA to go first (e.g AGP vs PCI) in your bios. So you could have your arcade monitor hooked up to the second VGA card, which would only kick in once XP had booted and run the drivers. You would be able to set the 2nd VGA card as your primary in XP. Again, you would see nothing on your arcade monitor until XP is booted.