CHKDSK Reports Corrupted Disk Space

    I found this problem in one of the computers I maintain.  The hard disk seemed to be getting full and I needed to free some space but looking at the disk reports there were some serious inconsistencies which made me take a closer look.
    The system is Win XP Pro SP3 with the disk formatted as NTFS.  Adding up all the space used by files as reported by Windows Explorer added up to something like 30 GB less than the total used space as reported by using the disk properties. 
    Running chkdsk reported

CHKDSK discovered free space marked as allocated in the master file table (MFT) bitmap.
CHKDSK discovered free space marked as allocated in the volume bitmap.
Windows found problems with the file system.
Run CHKDSK with the /F (fix) option to correct these.

    Running CHKDSK with the /F (fix) option at startup would not correct the problem.  It would say it was correcting it but the problem continued.  My suspicion was directed to the System Volume Information folder which is where the System Restore information is kept and which is not accessible to Windows Explorer.  My suspicion was that it might be corrupt and that even CHKDSK could not fix it.  My suspicion was further enhanced because this system had recently got a nasty trojan which took a lot of work to get rid of.  I figure that the cleaning had detected the trojan files hiding in the system restore area and had cleaned or deleted those files but this action resulted in a corruption of the System Restore folder and files.
    I disabled System Restore and ran CHKDSK several times and finally everything was the way it should be and 30 GB of disk space were freed.  I then enabled System Restore and created a new restore point.
    Then I connected the drive as a secondary drive (boot from another drive) and ran CHKDSK again and it came up with no errors. I found that if I boot from the drive being checked in the end it comes up with errors, probably because the drive is being written to while it is being checked.