I don't have a solution for you but I will share my experiences along
the same lines.

I have two computers that run XP and have drives configured in removable
trays. I installed Ubuntu 8.04 on the first machine using a brand new
drive in the removable tray. I retained another drive on a second
removable tray that was formatted with NTFS. In addition, I had a USB
thumb drive online.

I was initially delighted that Ubuntu came up perfectly and recognized
my NTFS drive and my USB stick right off the bat. I had fun reading and
writing to the NTFS drives from Ubuntu with absolutely no problem.

Then suddenly, I started getting an error when I rebooted. The error
centered around Grub not being able to load the partition. It wouldn't
allow me to load anything.

Pulling the Ubuntu drive from the tray and restoring the XP boot drive
worked fine.

I deleted my Ubuntu partitions on my new drive and freshly installed
Ubuntu 8.04. The same thing occurred.

I wonder what I can do to prevent Grub from installing in the first
place? Do I need this if I do not want multiple OS's on the drive?
Should I install Ubuntu initially with all of my NTFS drives out of the
system?