NtBackup only backing up part of some folders - error in logs

I have a Windows 2003 backup server with a RAID subsystem that I run NtBackup batch files on to backup our Windows 2003 server files.  I am having a problem backing up a web server in our DMZ.  The web server has more than 40,000 files, but when I run the scheduled batch file from the backup server to backup the web server files to its RAID hard drives, the backup ends without backing up all of the files in a couple of the folders that have more than 15,000 files each.  The web servers used to backup without an issue, but now its having problems backing up.  These are the errors from the NtBackup log.

Could not access portions of directory \\192.168.100.55\D$\files\ppol
You may not have permission to open the file, or the directory may be missing or damaged.
Please contact the owner or administrator.

Could not access portions of directory \\192.168.100.55\E$\files\eeob
You may not have permission to open the file, or the directory may be missing or damaged.
Please contact the owner or administrator.

I normally run the backup with a user with backup operator rights, but have tried running it giving the user administrator rights and it returns with the same results.
SmeglorAsked:
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SmeglorConnect With a Mentor Author Commented:
I found a work-around.  The server backs up fine from the DMZ side, but runs into problems when backing up from LAN to DMZ on a file-by-file basis.  So We just back everything up on the DMZ side, then copy the single backup file from the DMZ to the LAN backup server.  
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xfreddieCommented:
Sounds to me that maybe you harddrive is going bad.

Have you checked the drive for errors?

Goodluck,
Xfreddie
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SmeglorAuthor Commented:
The web server is a VM running on a RAID host so I dont think I can do checkdisk on it safely.  If I do a local full backup on a small number of files on the web server, it works, but I cant do a full backup locally on all the files because I dont have the drive space.  I need to have the full backup run from the backup server.  Whats weird is that sometimes the full backup will be 10GB or 7GB, or 12GB, or 5GB.  Not the full size it should be, but it seems to be backing up more or less files, but its not consistent.
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mmarsmanCommented:
You aren't running out of space on your backup server are you?  I've had a similar error when running disk to disk backups when capacity has been exceeded.

Matt
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