I had exactly the same problems as you descibed. I finally managed to fix my problems using the following tutorial on solving grub-problems:
http://www.linuxforums.org/tutorials...ial-19999.html
I did the following:
- Create a Grub boot diskette (see section 'Getting a Grub boot diskette')
- Boot from the floppy
Then within Grub
- Find the grub.conf file on your second disk (find /grub/stage1 or find /boot/grub/stage1)
- Load this grub.conf file (configfile (hd1,0)/grub/grub.conf)
Check if all works well, then make it permanent on the MBR of your first hard drive
- setup (hd0) (hd1,0)
This is how it worked for me. I'm not an expert, so please refer to the tutorial. My example works on my machine (with /boot on the first partition of the second disk)