Thanks for the help,
What you are saying makes a lot of sense. My current power setting is set to turn off the hard drive after 20 mins of inactivity. Since I previously only had one HD which had the OS on it, it was never inactive thus I never experienced the slow downs. But now since the new HD is not constantly being used, it is very possible that it is being shut down after 20 minutes.
Anyways, is turning this power saving setting off a bad thing? Does it harm the drive or the computer?
My other specs:
E6600 overclocked to 3.4GHz
4GB of RAM on 32-bit Windows 7