booting problem, part II

I decided to make a separate thread rather than unburying the old one because I think I have a better idea and don't want to confuse anyone with the other information.

I've taken a closer look at the Event Viewer, and when I first started noticing problems (the ones I mentioned a couple months back) I was getting:

Event ID: 11
"The driver detected a controller error on \Device\Harddisk1\D"

Eventually I think that one SATA outlet on the mobo that connected to my non-OS hard drive crapped out (I have two hard drives), because not too long after it wasn't being detected. I moved the SATA cables and everything seemed fine. I was still getting the error, though, up until recently. Now I'm getting this:

Event ID: 55
"The file system structure on the disk is corrupt and unusable. Please run the chkdsk utility on the volume D:."

This error is logged once, then again about a minute later. Volume D: is my non-OS hard drive, and once I boot there doesn't seem to be any problems with it. I can move large files and do other stuff without it complaining.
The system's taking much longer to boot, though. It gets past the logo loading screen, then hangs at a black screen for a couple minutes before loading the login screen. The hard drive LED blinks...blinks...blinks...blinks a couple more times...solid for a good minute or two before loading the login screen.
I ran the Recovery Console through the CD and tried "chkdsk" on my OS drive, out of curiousity. I got the "appears in good condition" message. Then I "chkdsk"ed the problematic one (the non-OS drive), and instead of "good condition" it did "performing additional checking or recovery..." I ran a "chkdsk" before and it said it was fine, but now every time I check the drive it performs additional checking, which I'm assuming is "chkdsk /p" (check even if the drive isn't flagged as dirty). I then did a "chkdsk /r" hoping it would deal with any bad sectors. After a while it finishes, yet after running "chkdsk" numerous times it never says "good condition." It never tells me about "one or more errors", though.

My hard drive is a Hitachi Deskstar T7K250. I tried running the SMART diagnostics in Speedfan and ran the Hitachi Fitness Test via boot CD (Advanced). Both came up clean. I did notice that both drives were listed as Master. If my non-OS hard drive was Slave, would it not be read (or at least not as much) on boot, possibly helping this problem?
Also, regarding switching the jumpers to Slave, I read that doing this could potentially shrink the hard drive capacity. What are the chances of this, and does it just make the other portion inaccessible (so if I switch back to Master it'll come back) or does it also erase the data?

Any other recommended diagnostic tools I should try?
I'm pretty sure the non-OS hard drive is to blame (since the errors refer to just that one), but how to deal with this issue, I don't know where to start. I tried updating the SATA RAID controller driver (I don't use RAID, but I read it could be a culprit), to no avail. Performing Chkdsk like the error recommends doesn't help, either. Any thoughts on this? Would a reformat clear it up, or would it be more of a physical hardware issue?

 

Hi ShockTroop,
If you have or can borrow a Norton System Works cd - even an older one, you can run their disk doctor directly from the cd. I've had really good experiences with it finding bad sectors and rerouting things that were getting stuck. The last time I used it, my computer was taking around 4 hours to boot up, so it was definitely in trouble. I expect there are other tools like that one, that examine the disk for physical defects and create fixes, but I happened to have that one and it did the job.
abri