I am also having this issue. I came from a Fedora installation, where everything in /home was kept from Fedora (different partition from /). After the install, I had some config issues (particularly sound), so I rebooted into Live CD and deleted most config files (some needed to be kept, common sense) in ~/.config, ~/.local/share, and ~/.[c]cache, plus a lot of hidden folders in the root of my home folder.
After that, things seem to be running more smoothly, however the issue the op stated has now come to attention. I thought it had to do with the gdebi packages, but "sudo dpkg-reconfigure gdebi gdebi-core" doesn't seem to help at all with this issue.
As with the op, any suggestions to fix this?