Hard drive "pausing" on boot/sleep mode

[Arkyte]

I've been having an intermittent problem for a couple weeks but now it seems to be happening all the time.

When i first boot my Windows 7 Ultimate (64bit) system, after logging in the hard drive reads for a second or two. It then stops for 3-4 seconds like it’s paused and then reads again. This goes on for 10-15 minutes then suddenly starts reading functioning normally. When it's "paused" I can move the mouse but can't click on anything. BUT if i do click on something when it resumes running for those few seconds it'll complete the operation.

Before it was just when booting now it seems to do it every time it comes back from sleep mode. I've looked around but can't find anyone with a similar problem. I'm running a WD Raptor 150GB HD. I've scanned it and it comes back perfectly fine.

I'd love to get some ideas about what is causing this issue.