You use this program to generate the monitor test patterns (ok, they're TV test patterns, but it's the same thing).
You MUST be using your AVGA card on your arcade monitor when you run this program. There are brightness adjustment slides, with instructions on the top of the screen that tells you exactly how to adjust your brightness and contrast to achieve the proper levels.
I just re-read your post, looks like you've used this software... ugh, silly me I must have missed that point even though I quoted it in my first reply! no points for being braindead for a moment :-)
Anyway, if it's just in Windows that you're seeing the issue, take a peek at your video settings, particularly GAMMA. You might have the GAMMA turned up way too much. Generally I don't have to touch those settings for windows.
If it's perfect in your front-end, and games.... Hmmm, dunno if I'd worry too much about it then, but I guess it would bug me a bit