Same here
Damnit!@# Got the same problem today.
System specs:
-Windows XP Pro
-Mobo Chipset: Intel i845PE
-Ati RadeOn 9800 Pro
-Seagate 7200RPM 160GB
-Seagate 7200RPM 200GB
-no raid controller installed
-The two error partitions are both NTFS on seperate HD's. One is 105GB, the other is 183GB. Both contain a lot of small files.
Before the problem:
Had I no problems until I reinstalled Windows XP. My previous XP installation was Windows XP SP1 and SP2, with no HD problems.
Just before the first bad partition:
Today I did a reinstall. I installed Win XP Pro (without SP's) with almost no drivers installed other than the default XP drivers. Then I installed the Ati drivers of Intel Chipset drivers. I don't remember which one I installed first and don't remember if I rebooted between or before these drivers. After installing one or both of these drivers, I rebooted and got the first Chkdsk problem during the startup. An error with index $0 or something like that. Because the test was taking a lot of time, I did a cold reset during the test. (I know this is usually a bad idea, but I didn't trusted the test because I couldn't see any cause which might have caused those index problems.)
The first bad partition:
The index errors were on my 200GB HD, on the 183GB NTFS partition, which contained a lot of small files. Some directories on this partition where not accessible, Explorer gave the error:
J:\Data is not accessible.
The file or directory is corrupted and unreadable.
There wasn't a clear pattern in which one was accessible and which one was not. I also hadn't used this partition yet, in the new XP installation.
Just before the second bad partition:
I backup some files on the bad partition to another large partition the other drive (G

. After backing the directories which could be saved, I did a Chkdsk.exe /F J: in the command prompt. I took a lot of times (3 hours?), and thousands of thousands files where "orphaned". After Chkdsk, the directory structure was recovered. Files were assessible and OK, but some files were corrupted!@#&*!@&.
Here some of the last (of the tons of lines):
Recovering orphaned file 728311~1.JPG (822958) into directory file 637018.
Recovering orphaned file 7283119rvhkojes.jpg (822958) into directory file 637018
.
Recovering orphaned file 58053O~1.JPG (823053) into directory file 637018.
Recovering orphaned file 58.053odgxgnbc.jpg (823053) into directory file 637018.
CHKDSK is verifying security descriptors (stage 3 of 3)...
Security descriptor verification completed.
Correcting errors in the master file table's (MFT) DATA attribute.
Correcting errors in the master file table's (MFT) BITMAP attribute.
CHKDSK discovered free space marked as allocated in the volume bitmap.
Windows has made corrections to the file system.
192788000 KB total disk space.
185608304 KB in 799057 files.
398076 KB in 23944 indexes.
0 KB in bad sectors.
764144 KB in use by the system.
65536 KB occupied by the log file.
6017476 KB available on disk.
4096 bytes in each allocation unit.
48197000 total allocation units on disk.
1504369 allocation units available on disk.
The second bad partition
After this, I installed some other software and drivers on my new XP installation. Also SP2 and a newer Intel chipset driver. After this, I rebooted and again, a corrupt partition!#@!@& This time it was on the other drive, the other large partition on which I backupped some files of the previous bad partition. This second corrupt partition contained large files (>100MB) instead of small files, but since I backupped files from the previous bad partition to this partition, I did contain a lot of small files. And only the Backupped directory on this second bad partition, is corrupted.
What I think what might be the cause:"
-If it's a hardware problem, than it might be because I moved the PC a bit (only 30cm), while it was running. But I doubt it.
-I think it's a software problem, because my previous XP installation never showed a problem like this before.
-I think it might be a driver (IDE?) problem maybe in combination with large NTFS partitions.
-Maybe I copied the problem (bad MFT atributes?) from the first bad partition to the second partition.
More info about MTF:
http://www.ntfs.com/ntfs_basics.htm
http://www.ntfs.com/quest14.htm
Q: How do I repair a corrupt master file table?
A: It rarely happens that MFT becomes corrupted. NTFS stores a copy of MFT that is called MFT mirror. If problem occurs, NTFS tries to synchronize these copies.
You can try to run Check Disk utility from Windows environment. Or if Windows is not bootable, boot from floppies or bootable CD-ROM to Recovery Console and run CHKDSK utility that could help you.
If the damage to MFT is serious, standard utilities might help you and you'll see "Drive cannot be accessed" message when trying to access the drive in Windows Explorer. In this case we recommend you to use third party software, like Active@ UNERASER for DOS or Active@ File Recovery for Windows to access and save your files to another drive, and then reformat the partition
http://www.forensics-intl.com/def11.html
http://www.pcguide.com/ref/hdd/file/ntfs/archMFT-c.html
http://support.microsoft.com/default.aspx?scid=kb;en-us;Q174619
"How NTFS Reserves Space for its Master File Table (MFT)"
The NTFS file system contains at its core, a file called the master file table (MFT). There is at least one entry in the MFT for every file on an NTFS volume, including the MFT itself.
Because utilities that defragment NTFS volumes cannot move MFT entries, and because excessive fragmentation of the MFT can impact performance, NTFS reserves space for the MFT in an effort to keep the MFT as contiguous as possible as it grows.