I boot using an old Win98 Boot Floppy to DOS, the following drives are usually detected
 
A - Floppy
C - FAT32 Partition 1
D - FAT32 Partition 2
E - MS RamDrive
F - CD Drive
 
on C there are two unattended setup files - unattend.txt and defaulthide.txt (the latter being almost identical to the former, except UnattendMode is set to defaulthide not fullunattend)
 
I go to F\I386 and type
 
winnt s"F\i386" u"C\unattend.txt"
 
to start the installer. The installer copies files, gets to the end then reboots. When next it boots, it boots GRUB (Linux Bootloader).
 
Boot sector virus protection is off in BIOS.
 
My suspicions for the cause of this problem are to do with my partition table. DOS doesn't seem to like it, and I am not letting DOS FDISK near it again (manually reconstructing my partition table was *NOT* my idea of fun). Reformatting D results in an error at the end about my partition table being "corrupt"
 
What DOS might dislike about my partition table (although AFAIK its supposed to support up to four primary partitions), is that there are two primary partitions then an extended partition (containing all my Linux stuff).
 
Any advice would be appreciated.