You may need to restore Grub as it is common for an installer to have more bugs than the distro itself.
The Fedora installation has a rescue mode with which you can boot into terminal mode. Perhaps the easiest to restore Grub in such a case, assuming your new FC6 partition is (hd0,2), which is sda3 in Linux, the command would be
Make the necessary adjustment if your new FC6 is in another partition. For booting from a USB disk MBR the setup should always be (hd0).