Drive Problem/Computer Freeze

Here’s my problem, sometimes when my computer first starts up I get intense drive activity (have 3 HDD’s and an SDD) that lasts for 2 minutes. This doesn’t happen every time only about 30% of the time. Also when I’m browsing or using a low cpu intensive program I get the same 2 minute freeze with intense drive activity. This doesn’t happen when I’m playing a game, but if I alt-tab out it might happen. Any ideas what maybe causing this? I’m thinking of nuking my computer and reinstalling Win 7 but wanted some advice on what might be the problem and saving me a reinstall.

My drives are:
2Tb Western digital HDD; primary gaming drive
1Tb Western digital HDD; used for all other programs and USER folders
1Tb Seagate HDD; Not used for much, don’t trust it.
128 Gb Intel SSD; os (Win 7) drive.