I had a similar problem. NT bootloader likes to control the system and load bootsectors from a file. You should be able to solve it with the following.
Boot into Linux (use a rescue disk if your machine does not boot into Linux) Install Lilo on the LINUX PARTITION use dd to copy the boot sector from the linux partition to a file dd -if /dev/hda2 -of bootsec.lnx -bs=512 -count=1 (replace hda2 with the location of your Linux partition) copy the bootsec.lnx file to a floppy boot into Windows NT copy your bootsec.lnx file from the floppy to the c: drive add the following to the boot.ini [operating systems] section multi(0)disk(0)rdisk(0)partition(1)\BOOTSEC.LNX="Linux" (replace the number in partition(1) with the proper partition number for Linux - NT starts at 0=hda1, 1=hda2, 2=hda3 if memory serves me) rumor has it that you need to update the bootsector file whenever you update your kernel. Here is my boot.ini file: [boot loader] timeout=30 default=multi(0)disk(0)rdisk(0)partition(1)\WINNT [operating systems] multi(0)disk(0)rdisk(0)partition(1)\WINNT="Windows NT Workstation Version 4.00" multi(0)disk(0)rdisk(0)partition(1)\WINNT="Windows NT Workstation Version 4.00 [VGA mode]" /basevideo /sos multi(0)disk(0)rdisk(0)partition(1)\BOOTSEC.LNX="Linux" Good luck, Pat