Noticeable slow downs after hdd installation

I wasn't sure where to post this so I put it here, sorry if it should be elsewhere

I just installed a new 1tb hdd in my system and I've been noticing slow downs with some programs like ati catalyst and internet explorer. I have my OS and all my programs (except for a game or 2) installed on my 60gb ssd and I'm using the 1tb hdd as supplemental storage. Is the Hard drive the problem or should I be looking elsewhere?

System Specs:
Windows 7 Home Premium 64-bit
OCZ Vertex 4 60gb ssd
Seagate Barracuda 1tb hdd
AMD FX-8150 cpu
G.skill Ripjaws X series 2x4gb memory sticks
Asus M5A88-M Motherboard with built in Radeon 4250
Hauppauge Colossus capture card
Pioneer BDR-2207
Thermaltake Lanbox Lite Case

Everything seemed to run fine before I installed the hdd but idk if it's the drive itself or maybe how I formatted it (i used windows disk management to format instead of the disk that came with the drive because the disk was corrupt). I moved a couple folders (Documents, Videos, Pictures, etc.) onto the hdd. I also got the "master boot record not found" error a couple days after installation which i was able to fix with the OS installation disk.

Any help anyone can give me would be much appreciated.
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More about noticeable slow downs installation
  1. Do you know whether the drive is running in ACHI mode or IDE? Check the BIOS to see the drive mode. Backup all data on the secondary drive if you decide to change the drive mode.
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