Secondary HDD making games lag/ Graphics card selection help

[Zipppy]

I have 2 HDDs in my PC, both are set up the same, but they have different performances in gaming. I used to have two WDCs, but the mainboard shorted out somehow on the secondary one, so I got a Seagate Barracuda of the same size (320 GB) and RPM (7200) from a spare parts box in the basement as a temporary replacement, and since then, the games installed on it lag.

The ones affected the most are Rigs of Rods, Source engine based games (TF2, HL2, etc.) and Crashday. I've noticed when this sort of lag occurs, the CPU usage drops drastically, from 60% to 10%, at least in RoR, and the game becomes unbearably laggy.

the HDD is well defragmented. I've checked with Smart Defrag 2 and the built in utility in Windows. I've installed some games on the primary, and they run better than they did on the secondary (Crashday improved the most). The primary is a 160 GB WDC WD1600JS which has 40 GB free, the secondary one, the Seagate, has at least 130 GB free.

I may call WDC up to see if they can replace the board, but it was made in 2006, same time the WD1600JS was made.

Any ideas on why this could be happening?

Just as a side note, I'm temporarily using a 7600GT, since my 9600GT overheats after 5 seconds, so I'm asking for card suggestions as well. I'm not sure about which brand to get. ATI has the best bang for the buck, but Nvidia is reliable from my experience.