Rtman6 is your second harddrive connected to the onboard IDE controller? Or are you using a 3rd party IDE controller? Sometimes drivers are the cause for trouble (I once had Promise controller that made my mouse jerky every few seconds). Why don't you disconnect your 2nd drive and see if Windows behaves fine afterwards. If it does, you know where to look for the problem (try different drivers, check HDD settings, use different controller).
Also, did you make sure that your 2nd drive has DMA enabled? To check do the following:
Go to Programs | Administrative Tools | Computer Management.
Then open the IDE ATA/ATAPI controllers tree the right pane and double-click on the Primary IDE (or Secondary IDE) Channel.
In the dialog that comes up, select the Advanced Options tab at the top. Under Transfer Mode select DMA if available.
I think if you are using a newer system like Win XP, this setting should already be default.