I've run into this problem where GRUB won't boot from a fresh Windows HD installed as secondary. The problem seems to be that Windows will only boot from the primary hard drive.

You can trick it by adding this block to your /boot/grub/grub.conf
title Windoze
map (hd0) (hd1)
map (hd1) (hd0)
rootnoverify (hd1,0)
makeactive
chainloader +1
boot

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