I think it's because of Grub 2nd release that requires specifical
conditions for working properly. Indeed that release of Grub
takes more place and can cause an overloading of the disk
boot sector (only 512 kb).
For having it working great, it's necessary
1) to boot from your master drive of course
2) to have Ubuntu on your 1rst partition (Grub in it for the minimum).
You can try this : use a partition manager, for example gparted
(live CD for being out of the system)
Set active the first partition of the drive where Ubuntu is
(so it will indicate the master disk boot sector to boot from the slave
disk)
Hope it will work with your configuration, if not you'll probably have
to change physical configuration (pins or dil swiches) for inverting
master and slave and maybe confirm in the BIOS.