or it could be corrupted indexes/sectors on the hard drive too. Could try running a chkdsk /F or /R on the drive that FFXI is installed on:
****NOTE: THIS IS FOR XP...VISTA/WIN7 USE A DIFFERENT DISK CHECKING UTILITY
Start/Run, and enter CMD in the box and hit <ENTER> to open a DOS window.
Then type the appropriate command, "chkdsk C: /F" or "chkdsk E: /F" followed by <ENTER>.
(/F is faster, but it doesn't check the sectors, just the files for corruption. /R checks sectors also, so you could run with /R instead of /F for a more thorough check if you like).
By running it in the DOS window like that, you will see the results when it finishes if it doesn't require a reboot to run. If the drive is flagged as a system drive (C: will be because that is what Windows is on, E: could be also if there is something it needs to access in real time like part of the swap file, etc.), it will prompt you to run it on reboot. If so, let it schedule it and then restart the system. If running on reboot, you will need to keep an eye on the messages while it runs. Just as it finishes it will state if it found errors or not (may go by real fast if running on reboot). If it found errors, run it again until it doesn't report it found errors. If you missed the message at the end, run it again just to be sure.
***Note: You may see the progress indicators go back and forth during the process (count up to 80%, then drop back to 55%, etc.). This is normal for it to do this. If by chance it is unable to correct all errors on the drive during a reboot, it may run it again the next time you reboot--so, it is kind of idiot proof in that regard...eventually it should fix all the errors after it reboots a few times.
If after several passes it is still being marked as "dirty" and running the check with each reboot, you potentially have some problems with sectors on the drive and will need to run it with the /R command to check all sectors and try to recover data. This is the only way to make it reset that dirty bit and ultimately stop the check on reboot--but it might take a few passes to fix everything. If this is the case, you would be better off booting from the installation CD (if you have one) and going into Recovery Console to run the commands there until it stops finding errors.

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