|No the boot.ini is correct in both cases.|
I would suspect the 2nd drive was not installed in this system.
The system utility which is doing just like you would do if you used the system bios to designate which drive is bootable, simply tells the system which is the bootable hard drive.
In this case, no matter which you designate as bootable, each drive will come up as c:
Are you using partition magic's pqboot.exe?
If the 2nd drive is as I suspect a repair install will correct the bootup.