Yesterday I installed FUDUNTU. During the install my MBR (I use ubuntu as my main OS) was overwritten. When I recovered the MBR I discovered that FUDUNTU was not listed. Any idea?
Fedora and Fuduntu use (as far as I understand) - legacy Grub.
I would restore Grub 2 to your MBR using your Ubuntu Live CD, then boot with your Fuduntu live CD (I'm presuming there is such a thing) and install Grub onto the root of the Fuduntu partition - please ask on the Fedora/Fuduntu forums on how to do this if you are unsure how to reinstall Grub into the Fuduntu partition.
Reboot into normal Ubuntu and re-run
This should put both Funduntu and Ubuntu into Grub 2