According to ultimarc's website, the AVGA is also available in a PCI express version. So you should be good to go on an upgrade if you want to buy that.
Do you need your AVGA? Doesn't sound like it to me if you are just going to do 640x480. Any graphics card can do that, so I wouldn't spend the extra money.
BUT, I would just keep on trying with the native res's until I got it right. You should post in the monitor forum about your sync issues and they will help you out.