I currently use xubuntu for my programming (in vmware), and can install ddrutility 1.6 on both 32 and 64 bit versions of 12.04. I will have to download and install the regular ubuntu 12.04 to test and see if I can recreate the issue, but I have a few questions. Is your ubuntu up to date with updates, or is it a fresh install? Is it the 32 or 64 bit version? Did you download it from here, or set it up through launchpad? Is you ubuntu really 12.04, or did you let it upgrade (type "lsb_release -a" in a terminal window to see what version you have).
You should still be able to use the .sh file as an alternative. Just read the help file on how to use it. Note that it has 3 requirements that you have to install, they are listed in the help file.
EDIT:
It is possible that the update server your ubuntu installation is connecting to is corrupt. Do a search for "ubuntu change update mirror" for how to change the update server mirror, and see if that solves your problem.
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