Limits,
You didn't mention if what version of Windows your running. There are a couple things that would come to mind. When you say "grinding" do you mean physically grinding or HD thrashing? Is it possible the system HD is heavily defragged? Also, usually you would want your fastest drive (SATA) as your system drive. Also, I notice you mention that you have two IDE drives one with Windows installed. Are two the HD's sharing and IDE cable as a slave and master? It would be advisable to make the drives each a master on their own IDE channel for best performance. In an ideal world, I would probably install Windows on the SATA drive, and use the other two drives for data as the faster the system drive, the faster the entire system is.
I hope this helps,
Jason