Your bootloader is not configured right. I've had nothing but grief running with Windows on the first drive and Linux on the second, so I swapped 'em. My preferred installation now. Makes life easier. To boot to your Windows, you can enter the stanza:
and it'll give you an easy 2 drive 2 boot. That is, if you use LILO.
That said, I mean swap your drives and install LILO to the Linux MBR. You'll lose your grief.