Did you install your boot loader (either lilo or grub) on the MBR of your Primary Master device? It sounds like you might have installed it on the root partition instead. You need to configure your boot loader correctly and specify the partition that windows is on, not just the hard drive.
Here is how the IDE devices work in Linux:
/dev/hda = Primary Master
/dev/hdb = Primary Slave
/dev/hdc = Secondary Master
/dev/hdd = Secondary Slave
The partitions then go in order according to the order of the partitions, hda1, hda2, hdb1, ...etc.
do 'fdisk -l' to get more information on what each partition is labled and then use this info to configure your boot loader.