ChkDsk message prevents boot of Server2003

I came in on Saturday after a scheduled reboot of my 2003 Server to  find a loop running on the monitor: Deleted invalid filename 0? (3031) in directory 536870912. Subsequent reboots bring up the same loop if I allow ChkDsk to run. If I bypass ChkDsk, the server boots fine; all data seems to be intact. and all the services and server functions run fine. This server has a  RAID controller with Diagnosis software; A RAID verify found bad data and rebuilt successfully, but did not solve the problem. I suspect the "invalid file name references something in the boot sector, since the loop starts within a minute or two of the ChkDsk starting. The only issue at this point is that I like to run a scheduled reboot every week just to keep the server fresh, and that won't happen if this ChkDsk hangs with the message.  Any help would be appreciated.