Here is what I do:
Set Windows to display at 800x600 (and 85 Hz but that's optional).
Adjust Windows desktop to be full screen.
Edit MAME.ini to have the following settings:
hwstretch 1
resolution 800x600
keepaspect 1
That should fix it. If it doesn't, you might try using Multires from
www.entechtaiwan.com. This will try to "Lock" the refresh rate at 85 Hz.
Apart from this, if you are using an ATI card, the driver may say it is outputing 85 Hz and actually be displaying 60 Hz. There is a registry change to fix this.