Firstly, I'm assuming that under 8.04 the dual-boot with
2 separate drives worked ok for you (allowing to select either OS).

It's possible that since you're using 2 different drives, that
GRUB got installed in its default configuration, and even
though these days, installing GRUB is safe to do with
dual-booting (provided it picks up the OSes you need)--

I am thinking that still it should allow you to use
the keyboard to arrow key and select something other than
default (Top of list).

I'm pretty sure you can edit GRUB on your HD -

You may/(may not) need to put a LIVE CD in your drive
and boot from it, and then under root privileges perform
necessary edits to your grub menu ("menu.lst" or "grub.conf") depending
on which version of GRUB you have.

Here's are forum links detailing dual-boot.

http://ubuntuforums.org/showthread.php?t=210409
www.linuxquestions.org/.../editing-grub2-207\
616/

You can edit it by this method

#
Step 1

Boot Ubuntu, login as a user and start a terminal session.
#
Step 2

Make a copy of the GRUB menu file as a backup by entering "cp
/boot/grub/menu.lst /boot/grub/menu.lst_BU." Use this file to restore
menu.lst if the changes fail.
#
Step 3

Edit the menu using the command "sudo gedit /boot/grub/menu.lst."
#
Step 4

Count the number of possible operating system choices. For example, when
first installed Ubuntu will be the first O/S in the file. Lower down in
the file will be Windows XP. Count other operating systems, if installed.
#
Step 5

Find the line "default = 0." Grub sets the default to boot the O/S
located as the first (0 relative) in the file menu.lst.
#
Step 6

Change the line "default = 0" to "default = 1." Save the file and exit.
This changes the default from Ubuntu to Windows XP. Ubuntu appears first
in the file and first on the menu display. Windows XP is further down in
the file and appears below Ubuntu on the menu display.
#
Step 7

Restart the PC. Let the GRUB menu take the default to verify the change
. The default is now set to 1 which means Windows will boot when no
choice is made.

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.

It sounds to me like you may be having a keyboard or keyboard driver problem. I
occasionally see this behavior when I try to boot with a USB keyboard attached
to my laptop through a powered hub.