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Fixing Problems with DOS Partition after Server Reboot

Novell Cool Solutions: Trench
By Malcolm Fisher

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Posted: 23 Jul 2003

With NetWare 5.1 running on a HP Proliant G2/G3, built with SmartStart 6.x, the DOS partition is sometimes inaccessible and the server will not boot: the DOS Partition is corrupted. This usually occurs without warning when the server is rebooted for any reason.


SmartStart 6.x modifies the partition boot sector on the DOS partition just prior to launching the NetWare install with the intent of making the drive bootable (similar to the DOS SYS command). Something during this process causes the CHS (cylinder/head/sector) information in the FAT16 boot record to become corrupted. This creates a lot of lost clusters and cross-linked files in the DOS partition. After a while, normal reads/writes to the DOS partition will step on a cross-linked or lost cluster, thereby resulting in corruption of the FAT table. Utilities such as Scandisk and/or CHKDSK will not fix this problem because of the incorrect CHS information in the boot sector.


  • Do not attempt this fix if you are running NSS volumes on NetWare 5.1 as it may render them inaccessible.
  • NetWare 6 can also use this fix, but I haven't tested it.


Backup the DOS partition File and Directory information. Reformat the DOS partition and then copy back the DOS files.

Compaq/HP have indicated that this issue will be fixed in SmartStart 6.4 due for release in August 2003.


  1. Create a backup of the existing server C:\ Drive if you want to prevent unscheduled downtime, or backup a C:\ Drive of another server which is running the same version of 5.1 Service Pack and DS Version.
  2. Create DRDOS bootdisk or an MSDOS boot disk
  3. Have a backup DOS Partition on a CD with the DOS partitions files and directory.
  4. Place the appropriate DOS Startup files (Autoexec and config) on the bootdisk complete with the correct DOS IDE CD driver.


  1. Boot Server using a bootable floppy disk created.
  2. Fdisk the DOS partition, and delete the primary partition.
  3. Create a DOS primary partitiion. Using your desired partition size. (max 2000)
  4. Make the partition active.
  5. Format the newly created partition with ' format C: /s '.
  6. Copy the CD contents to the newly formatted c:\ drive.
  7. Clean up any unwanted files from the root of the C: drive.
  8. Delete the SERVCFG.* files ( server registry files ) in the NWSERVER directory.
  9. Edit the startup.ncf file. (Make sure it is correct for the appropriate server model.)
  10. Edit the autoexec.bat and config.sys to ensure the server will start automatically on reboot.
  11. Check everything is ok and reboot the server. (Make sure to remove the floppy disk and the backup cd from the cdrom drive.)
  12. Check for errors while the server starts, as I had to re-copy a fresh FILESYS.NLM and CLIB.NLM which must have been changed/corrupted in the previous copies.

If you have any questions you may contact Malcolm at

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