ntfs erros when NTBackup runs

This happens on a Windows SBS 2003 Server.  Before I start there are no other known issues with this server...

Every night a few minutes into the SBS Backup this shows up in the system log:
Source: ntfs
Category: Disk
Event ID: 55

The file system structure on the disk is corrupt and unusable. Please run the chkdsk utility on the volume System.
40 minutes later the exact same Event is logged.  This only started happening a month ago.  It now happens, without fail, every time the daily backup runs.

What I've tried:
Looked at a lot of KB articles that didn't seem to apply to this situation.  One of them suggested running chkntfs at command prompt.  I did that and was told that the drive is "not dirty."  According to the KB article "no further action is required."  That's all nice and good but I don't want to just ignore these errors and pretend like nothing is wrong.

Before anyone suggests running chkdsk /f or /x, this is a live server and if I am going to take it down and possibly break it, it is going to require some planning.  What I think might be wrong is that there is 1 or 2 corrupt files that only get accessed when the backup runs.  If that is the case I guess it could just be ignored.

Any suggestions or thoughts?

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Lee W, MVPTechnology and Business Process AdvisorCommented:
I think you're asking for serious problems.  You're backups aren't working because there may well be something wrong with the disk.  You seem to be under the impression that "chkdsk" is designed to erase all your data in the event of a single file corruption.  The first sign of a problem I would have run Chkdsk (because your backups at the time were current).  Now you don't have current backups and if Chkdsk does correct things and cause some additional dataloss (which I've always been paranoid about but cannot recall ever having seen), you're really in trouble.

I would strongly recommend trying to robocopy your data off the server to have a more current backup, then run chkdsk.  Or take your chances that it might not be more symptomatic of an impending disk failure that loses EVERYTHING for you.

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monahansoloAuthor Commented:
The backups are fine.  I have done test restores to make sure.

If their is corruption in the MFT, chkdsk will make a mess of the server.  That is why I am asking for advice before running it.
Lee W, MVPTechnology and Business Process AdvisorCommented:
So you'd rather run with corruption that could get worse instead of fixing it?  I've done chkdsk commands plenty of times before and the worst that happened to me is a directory listing got messed up.  Run the command and rely on your backups.  

And are you SURE your backups are fine?  Have you done test restores?
chfdsk has saved my drives and never had a failer yet. It sure beat losing all the information.

You will need to fix the problem sometime, might as well get it over with. Sure makes you sleep better knowing that.

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