Ilija,
Just found this which looks promising - Bootpart. I might give it a try next time I install Fedora...
So, you've fixed your MBR with fixmbr from the XP rescue CD. And the original Ubuntu install is on another partition of your HDD.
Reads like bootpart will peel off an image of the boot sector of your linux install and whack it in your Windoze boot.ini. So it sounds like it automates the "fiddling" I tend to do each time, minus the need to boot into linux with a rescue cd, mount the system etc... Neat.
Here's an example of how it's done (Fedora example, but can't see why it doesn't apply to Ubuntu too - just change "Fedora" to "Ubuntu" in the bootloader name). Note that you need to know the boot sector of your linux - if you didn't create a separate /boot partition during install this will just be the / partition.
Anyway, the example looks fairly straightforward - I haven't used it so no personal recommendation. But it might just do the trick.
James.