You need to make sure you are running the very least number of applications in the background as possible.
If you are using Win98 the following works to see what's really happening and make changes. If you are on Win2K or XP, not sure if it works or not. I use it so much I made a shortcut on my desktop to it:
Go to Start> Run> and type msconfig.exe
A little program will pop up. Click on the Startup tab and you will see all the junk you have running in the background. Some will be obvious ones to turn off like hp sched and MS office. Others will be "spyware" you didn't even know were sending out information about you behind your back. Remove the check from the ones you don't want running and reboot. You'll need to leave SYS tray and task mon enabled, and your anti-virus software, ect. Gradually uncheck one box at a time and reboot, making sure everything is working ok until you get it down to a minimum.
On most computers you can also disable Config.sys and Autoexec.bat under the General Tab, Win 98 no longer needs them unless you still run old DOS programs.
Leave Win.ini and System.ini alone !
Also make sure your computer is set to use the monitor your actually using, not the default monitor. See my new post re:Direct X from ATi.
Hope this helps, let me know. Your system is very powerful, something is not right. My old P-3 600 does a lot better than that.