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When I install Ubuntu 8.10 on a USB HD, it messes up my MBR. You can fix this directly from the Ubuntu terminal. You do not need to use the live CD if your Ubuntu system starts.

You need to install a little program called ms-sys. It will rewrite your Master boot record (http://ms-sys.sourceforge.net/). The ms-sys package you get directly from their site does not install on newer version of Ubuntu (apt-get install ms-sys). You will need to use the debian package http://packages.debian.org/etch/ms-sys

Once ms-sys is installed, you need to figure out on which partition is located Windows

sudo fdisk-l

this will list the hard drives installed. You are looking for a line with NTFS as system. Something like:

/dev/sda1 1 9327 74919096 83 NTFS

You need to replace /dev/sda in the following command line with your device Boot (without the number)

sudo ms-sys -m /dev/sda

that's it! You can refer to the following page for more information:
http://www.arsgeek.com/2008/01/15/how-to-fix-your-windows-mbr-with-an-ubuntu-livecd/