Short summary:
I have some weird problems with harddrive corruption, always occuring after the bootconfiguration was changed. For example: trying to fix the Vista bootloader, fixing the XP bootloader ("fixboot") or also just installing XP. I always get errors on a different drive than the bootloaders or Windowses are. Chkdsk works 3 hours to restore apparently all files on a certain partition. It seems to restore the master file table which includes the folder structure. The line it shows thousands of times is "Inserting an index entry into index $O of file 27".

The whole story:
It all begun with installing a new SATA harddrive. It substituted an IDE drive, which only contains data partition (no operating system, primary partitions, bootsectors or bootloaders).

After the change my harddrive setup is like this: 1 IDE drive containing 3 WinXP installtions. They are booted by the standard XP bootloader/menu on the 3rd partition. 2 SATA drives, with only data (no operating system, primary partitions, bootsectors or bootloaders) on 2-3 logical partitions each, plus Windows Vista on the last partition of the last drive (in a logical partition, not a primary). All was installed before the drive change. The Vista bootloader took over booting either to Vista or to the XP bootloader, allowing me to select between my 3 XP partritions. This all worked fine without any problems.

After exchanging the 2nd IDE drive with the new SATA drive, I got an error from the Vista bootloader:
File: \Boot\BCD
Status: 0xc000000e
Info: An error occured attempting to read the boot configuration data.
I tried to repair it with the "System startup repair" on the WinPE of the Vista installation disk ... it didn't fix the error. So I restored the XP bootloader under XP's repair console by using "fixmbr" and "fixboot". This finally allowed me to at least boot into my main WinXP partition.

Now the weirdness begun. I always got bluescreens after a couple of minutes of running WinXP, usually when I accessed files e.g. creating a system restor point or just loading the Opera browser. After replugging the SATA harddrives from port 1+2 to 3+4 of my MoBo (ASUS A8N-SLI Deluxe), the bluescreens stopped. But then, after a while Windows reported a damaged file in a "baloon tooltip" and asked me to run Chkdsk. So I rebooted and check disk ran for more than 2 hours, repeating the line "Inserting an index entry into index $O of file 27", appallingly on the drive that contains "My Documents" with my most important files. Fortunately almost all files were restored in "found.000 and found.001" folders (including the folder structure).

After that, everything worked like normal. I did a few RAM test and looked at the disk's health with a SMART tool, but everything looked completely fine.

A few days later I once again tried to fix the Vista installation (as I only restored the XP bootloader until then), with 2 tools called "EasyBCD" and "VistaBootPRO", but I still got the same error in "\Boot\BDC". Also trying the commands "bootrec /fixboot", "bootrec /fixmbr" and ""bootrec /rebuildbcd" didn't help.

The it got weird again: as I booted back into XP, ChkDsk found a couple of errors again. Not as heavy as before, but still.

Now after a few more days, I decided to reinstall WinXP on one of the first 3 partitions ... and guess what happened ? Again ChkDsk did "Inserting an index entry into index $O of file 27" for 3 hours. The weird stuff being, ChkDsk only found problems on the SATA disks with only data on it, the IDE drive with the Primary partitions with Windows on were all fine.

I do know how bootloaders work to load XP and Vista. I'm using multiple operating system for years, but I just don't get a clue what is going on now. I could imagine Windows destroying a system disk while installing a new bootsector on the system drive, but that the bootloaders are installed fine, and errors are only on another drive is really strange for me. Is it a hardware problem, maybe a damaged IDE/SATA controller, or a software probelm ? Why does it only happen when doing stuff with the bootsectors ?

There seem to be some clever guys on this forums, maybe some one has an idea whats going on here. In any case, thanks in advance if you already read until here.