This problem could be a little complicated one. I had a 250 GB SATA HDD and an 80 GB IDE working together. I then came to know that the data write speed on the 250 GB HDD was not at all good and it had developed some bad sectors. This Hard drive had windows installed on it (XP). My other HDD had Linux on it (IDE) and it was working great. Since the 250 GB was under warranty, I got it replaced from Seagate. When I installed the second HDD I started having the same issue. I thought the problem was with the replaced HDD (it was a certified repaired HDD) and I got that replaced too.
When I got the third hard drive (This time Seagate gave me a new one), I installed it on my PC, made two primary paritions and when the first signs appeared of that trouble, I removed the hard drive for good. The first signs were that suddenly the read/write speed would drop down to insanely low levels (3-5 MB/s). I realized that maybe the problem lies somewhere else. I changed the Data cable, I changed the power supply and when I could afford it later, I changed the Motherboard, RAM and CPU (It was due for an upgrade anyway).
Now I have installed Windows on that hard drive in a completely brand new hardware setup and I see that the second primary parition of that HDD is giving issues. The read speed is going as low as 3-4 MB/s.
Now I am completely baffled because this is the new hardware. Could it be that this Hard drive had been damaged in my old system and I got it out too late? Can someone tell me what is going on Should I just go and buy a new hard drive.
It sounds like you have done everything with exception to replacing the hard drive. Since you symptoms lie within the write/read speeds, it is only logical to replace an inexpensive piece of hardware. Be sure to look at your secondary hdd configuration and make sure you do not have any conflicts. Your IDE setup could be causing the problem. Disable the IDE drive physically and check for symptoms. It appears you may have done all this already.