I have discovered a way to increase my FPS for SH3. Here's how you might be able to do it.
Increase your screen refresh rate to the maximum that your monitor will allow(mine is 80MHz). Note: WARNING!!! Do not set your monitors refresh rate over what the manufacturer max rating is. For instance, mine is 80MHz @ 1024 by 768. Check your owners manual or do a Google search for your monitors max settings.
Now, set your screen area to 1024 by 768 and thats it. You might notice now that your FPS has increased. Hope this works for everyone.
Edit: Also make sure that you uncheck the synchronisation option in SH3 as well.