Before upgrading my N800 to Diablo, I was booting from an (internal) 2 GB card, and I decided to switch to a 16 GB card. So after performing the flash, I download Fanoush's new initfs flasher for the dual-boot, and used Milhouse's script to do the cloning. (I had pre-partitioned and formatted the card)

When I rebooted, I got an error along the lines of
"Booting from immc2 (mmcblk0p2 ext2)...
Failed to boot from immc2, booting from flash ..."

I did everything I could to debug this, such as making sure bootmenu.sh didn't think it was ext3 or something, and re-mkfsing and cloning several times - all with no errors. I also noted that my old Chinook rootfs on mmcblk1p2 could boot just fine when I selected it from the menu.

Eventually I finally got the idea to switch (back) the two cards. Suddenly Diablo is booting from the 16 GB card in the external slot, no problems.

The really odd thing is that the 2GB card Can boot from the internal slot. Anyway I would rather have the 16 GB with Diablo be the internal one. Any suggestions would be very welcome.

It seems the problem was the specific A-data class 6 16GB card I was using. I still don't know why it would matter which slot it's in - esp. because it could read/write just fine in either, but maybe it was related to the power usage thing.