Win7 runs the bootup splash screen at 1024x768. Almost no arcade monitors (D9800 included) will handle this. The desktop also runs by default at 1024x768. When you set things for 640x480, make sure you check that it's running at 60Hz refresh. I think Win7 will run it higher by default. Your BIOS text should be visible if you have any (many brand-name PCs display nothing until Windows starts).
Windows 7 really assumes you have a monitor capable of much higher resolution. Most dialogs will be unusably large at 640x480 (they were even on XP), but it should be possible to make it at least run.