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Heh, I would post this under a specific hardware forum.. if I knew what was wrong 
The best way for me to describe this problem is to explain what I've tested so far .
Equipment: WD 160 gig HD, Seagate 80 gig HD, Promise Ultra 100TX2 Controller Card, working IDE cable from my other computer (to eliminate the possibility of faulty IDE cables).
The story first.. chkdsk messed w/ my WD drive and deleted/recovered many orphan files and re-did my indexes (I posted about this in the OS forum and have since "recovered" from the error). I've managed to recover 80-90% of the deleted files and have them sitting on an external HD right now so I won't risk losing them again. All other HDs with important data is unconnected so I don't accidently corrupt anything more.
So now what I did, in list format so it's easier to understand the chronological steps:
1) Full format WD Drive
2) CHKDSK the WD drive - no errors found
3) Copy recovered data back onto the WD drive
4) Disconnect WD drive from IDE1 and plug in into PCI Controller Card
5) Run CHKDSK on WD drive (while connected to PCI Card). Received error message:
> chkdsk f:
The type of the file system is NTFS.
Volume label is New Disk.
WARNING! F parameter not specified.
Running CHKDSK in read-only mode.
Correcting error in index $I30 for file 22941.
Correcting error in index $I30 for file 23065.
and so on and so forth. (I let a whole page of this go on before I ctrl-c it)
* At this point, I'm thinking my PCI Controller Card has a problem... so further tests
6) Plug WD Drive back into IDE1 (mobo controller) and run chkdsk again. 0 problems again.
7) Randomly pick 30-40 files on the HD to load and run, no problems at all
8) Download and run WD's own Diagnostic Tool, no problems!
9) Figure I'll just try again and plug the WD drive back into PCI Controller card.
10) Run WD's Diag Tool again and it won't even start! Says there's an error in the cable.
11) Switch to yet another working IDE cable, and still have the same error in WD's Diag Tool.
12) Plug WD Drive back into IDE1 only this time I grab a clean Seagate 80 gig drive and plug it into the PCI Controller Card. The Seagate drive comes from a working computer, the drive is working in the other computer, and I had just finished formatting the drive the other day.. meaning there's no data on it.
13) Run Seagate's Diag Tool on the drive (while it's plugged into Controller card) and it returns 0 errors.
14) Run CHKDSK on the Seagate HD and it returns 0 errors.
And this is where I am right now. A quick summary would be:
* WD & Seagate work fine w/ 0 errors discovered by both CHKDSK and respective company's diagnostic tools when connected to Motherboard IDE Controller.
* WD finds index errors by CHKDSK and can't even start WD diagnostic tool when connected to PCI Controller Card.
* Seagate finds 0 errors and works fine on PCI Controller Card.
Things I'm considering and will be testing:
* Dump some dummy data onto the Seagate drive and test w/ PCI Card.
* Is there a way the recovered data itself is causing the corruption? Test by re-formatting/deleting files off the WD drive and testing it on PCI Card again
- Sub-set of the above point woudl be that the CHKDSK error seems to be w/ index of files, so it's natural that CHKDSK finds no errors w/ the Seagate drive since there are no files to have index errors. Still doesn't explain why the individual company diagnostic tools said Seagate drive was fine while WD couldnt even scan.
* I thought maybe I had an old BIOS on the card that didn't support large HDs, but then I remembered that this is the PCI card that came WITH the WD hard drive. Also, I've been running a Maxtor 160 gig off that same PCI Card for no problem. I feel checking if the Maxtor drive still works on the PCI Card though cause it might corrupt the data like it did with the WD's data.
Anyway, could someone please help me w/ any tips or suggestions? Or maybe some behavior of some device which is "normal" and I'm thinking is wrong? (Hell, maybe chkdsk isn't meant to be run on a device conntected to a PCI card, I dunno).
[edit] Update:
15) Copied over 70 gigs of random files from the WD drive to the Seagate drive w/ WD on IDE1 and Seagate on PCI IDE Card.
16) Ran chkdsk and Seagate Diag Tool on Seagate drive, no errors!
17) Moved WD drive to slave of PCI IDE card.
18) Ran WD Diag and CHKDSK. WD Diag ran WITHOUT any errors!!! CHKDSK picked up index errors again.
19) Moved WD drive back to master of PCI IDE card.
20) WD Diag had the same error as before... couldn't get past "Running Cable Test." Get the error msg: Cable Test::Read diagnostics sector error!
What does this mean?! CHKDSK says HD is fine when on IDE1, but has index errors when on PCI IDE Card. And now, WD Diagnostic tool says it's fine on IDE1 or as a slave on PCI IDE Card, but has an error message when it's on master of PCI IDE Card!
[edit] Further update:
Well this is interesting now. I took a break and shut my machine off.. came back a few hours later and tried to run WD Diag again on a whim, and it started scanning! W/ my WD connected to PCI card!!! And it scanned fine! NO CHANGE AT ALL except letting my computer rest and it started working!
However, CHKDSK was still finding index errors. I guess something in me, subconsciously, had an inkling of what was going on though, so I downloaded the latest Promise IDE Controller Card drivers from Western Digital. That's what fixed it! Now I don't have index errors anymore on CHKDSK.
I guess I just didn't consider doing that because (1) My Maxtor 160 gig on PCI card has no problems in the past, so I assumed my WD 160 gig wouldn't have problems either, and (2) I always thought the drivers was for Windows to recognize the full 160, which it already was doing. I didn't think it would effect CHKDSK's index error detecting script.
Oh well, problem solved =) (hopefully, haha)
The best way for me to describe this problem is to explain what I've tested so far .
Equipment: WD 160 gig HD, Seagate 80 gig HD, Promise Ultra 100TX2 Controller Card, working IDE cable from my other computer (to eliminate the possibility of faulty IDE cables).
The story first.. chkdsk messed w/ my WD drive and deleted/recovered many orphan files and re-did my indexes (I posted about this in the OS forum and have since "recovered" from the error). I've managed to recover 80-90% of the deleted files and have them sitting on an external HD right now so I won't risk losing them again. All other HDs with important data is unconnected so I don't accidently corrupt anything more.
So now what I did, in list format so it's easier to understand the chronological steps:
1) Full format WD Drive
2) CHKDSK the WD drive - no errors found
3) Copy recovered data back onto the WD drive
4) Disconnect WD drive from IDE1 and plug in into PCI Controller Card
5) Run CHKDSK on WD drive (while connected to PCI Card). Received error message:
> chkdsk f:
The type of the file system is NTFS.
Volume label is New Disk.
WARNING! F parameter not specified.
Running CHKDSK in read-only mode.
Correcting error in index $I30 for file 22941.
Correcting error in index $I30 for file 23065.
and so on and so forth. (I let a whole page of this go on before I ctrl-c it)
* At this point, I'm thinking my PCI Controller Card has a problem... so further tests
6) Plug WD Drive back into IDE1 (mobo controller) and run chkdsk again. 0 problems again.
7) Randomly pick 30-40 files on the HD to load and run, no problems at all
8) Download and run WD's own Diagnostic Tool, no problems!
9) Figure I'll just try again and plug the WD drive back into PCI Controller card.
10) Run WD's Diag Tool again and it won't even start! Says there's an error in the cable.
11) Switch to yet another working IDE cable, and still have the same error in WD's Diag Tool.
12) Plug WD Drive back into IDE1 only this time I grab a clean Seagate 80 gig drive and plug it into the PCI Controller Card. The Seagate drive comes from a working computer, the drive is working in the other computer, and I had just finished formatting the drive the other day.. meaning there's no data on it.
13) Run Seagate's Diag Tool on the drive (while it's plugged into Controller card) and it returns 0 errors.
14) Run CHKDSK on the Seagate HD and it returns 0 errors.
And this is where I am right now. A quick summary would be:
* WD & Seagate work fine w/ 0 errors discovered by both CHKDSK and respective company's diagnostic tools when connected to Motherboard IDE Controller.
* WD finds index errors by CHKDSK and can't even start WD diagnostic tool when connected to PCI Controller Card.
* Seagate finds 0 errors and works fine on PCI Controller Card.
Things I'm considering and will be testing:
* Dump some dummy data onto the Seagate drive and test w/ PCI Card.
* Is there a way the recovered data itself is causing the corruption? Test by re-formatting/deleting files off the WD drive and testing it on PCI Card again
- Sub-set of the above point woudl be that the CHKDSK error seems to be w/ index of files, so it's natural that CHKDSK finds no errors w/ the Seagate drive since there are no files to have index errors. Still doesn't explain why the individual company diagnostic tools said Seagate drive was fine while WD couldnt even scan.
* I thought maybe I had an old BIOS on the card that didn't support large HDs, but then I remembered that this is the PCI card that came WITH the WD hard drive. Also, I've been running a Maxtor 160 gig off that same PCI Card for no problem. I feel checking if the Maxtor drive still works on the PCI Card though cause it might corrupt the data like it did with the WD's data.
Anyway, could someone please help me w/ any tips or suggestions? Or maybe some behavior of some device which is "normal" and I'm thinking is wrong? (Hell, maybe chkdsk isn't meant to be run on a device conntected to a PCI card, I dunno).
[edit] Update:
15) Copied over 70 gigs of random files from the WD drive to the Seagate drive w/ WD on IDE1 and Seagate on PCI IDE Card.
16) Ran chkdsk and Seagate Diag Tool on Seagate drive, no errors!
17) Moved WD drive to slave of PCI IDE card.
18) Ran WD Diag and CHKDSK. WD Diag ran WITHOUT any errors!!! CHKDSK picked up index errors again.
19) Moved WD drive back to master of PCI IDE card.
20) WD Diag had the same error as before... couldn't get past "Running Cable Test." Get the error msg: Cable Test::Read diagnostics sector error!
What does this mean?! CHKDSK says HD is fine when on IDE1, but has index errors when on PCI IDE Card. And now, WD Diagnostic tool says it's fine on IDE1 or as a slave on PCI IDE Card, but has an error message when it's on master of PCI IDE Card!
[edit] Further update:
Well this is interesting now. I took a break and shut my machine off.. came back a few hours later and tried to run WD Diag again on a whim, and it started scanning! W/ my WD connected to PCI card!!! And it scanned fine! NO CHANGE AT ALL except letting my computer rest and it started working!
However, CHKDSK was still finding index errors. I guess something in me, subconsciously, had an inkling of what was going on though, so I downloaded the latest Promise IDE Controller Card drivers from Western Digital. That's what fixed it! Now I don't have index errors anymore on CHKDSK.
I guess I just didn't consider doing that because (1) My Maxtor 160 gig on PCI card has no problems in the past, so I assumed my WD 160 gig wouldn't have problems either, and (2) I always thought the drivers was for Windows to recognize the full 160, which it already was doing. I didn't think it would effect CHKDSK's index error detecting script.
Oh well, problem solved =) (hopefully, haha)