does sound like a refresh rate swap.
As you are using 98 you can force one rate for all res colour depths like u can with w2k & xp.
Go through each res starting at 640x480 and work up to your highest res, do it for all colour depths (16colours, 256, 16bit, 32 bit/full colour) each time set the refresh rate to be the same as your current desktop eg: if your desktop settings ate 1024x768x32bit 85hz set 640x480x16 colour/256colour/16bit/32bit to 85hz
Another thing to check is what monitor driver you are using, windows normaly defauts to "Plug & Play" monitor, but you can find the correct inf drivers for you monitor at its website. load this up and choose the right one, then as one of the above posts says, select optimal for all.
Regards
Mandrill