At this point in time, 14+3 (there are two different failure signatures) packages remain affected. Here are my notes on these:

qbzr: This remains affected by fallout from the previous bug causing tags not to be merged from Debian. We have not fixed it up yet, because local testing has determined that the resulting import would be affected by another bug (picking the wrong upstream-* tag to extract as the upstream branch) producing contorted history.

clipit, gm-notify: Each contains only two package versions, the second in each branch committed by a human, with incorrect specification of the entire package version as the upstream version. My recommendation is to delete the branches from Launchpad entirely and redo the import cleanly.

python-configglue: Fairly similar to the above, there was an upstream version imported with the incorrect version number. As the branches include only 4 package versions across two upstream versions, and little interesting history, I recommend deleting these branches and redoing the import cleanly.

apport: A somewhat muddled awkward situation has arisen here, because, I believe, existing manually maintained branches have been designated as official package branches without fully considering the consequences for the importer and for the branch-distro process used when a new Ubuntu series is created.
Specifically, there exist lp:~ubuntu-core-dev/ubuntu/$series/apport/ubuntu branches for hardy, karmic, lucid, maverick, natty and oneiric, and this is where the actual development takes place. Of these, the maverick branch *only* is marked as an official branch. However, the branch-distro process appears to have created official branches for natty and oneiric at lp:~ubuntu-core-dev/ubuntu/$series/apport/$series - note the differing last component of $series vs. ubuntu. The human packagers have ignored these autocreated branches and created their own following their pre-existing naming convention.
In the short term, we should delete the spurious unmaintained natty and oneiric branches, shifting the official branch links to the branches that are actually being used. In the long-term, we need to do something to stop the situation re-occurring, but I'm not sure what.
The ~ubuntu-core-dev/..../ubuntu branches are in active use and are derived from the project's upstream VCS. As a result, the upstream version tags are just "VERSION" not "upstream-VERSION", and the importer does not understand this well.

langpack-locales: This branch is in active use for versioning the actual packages uploaded to the archive, but has had numerous new upstream versions manually committed directly to the packaging branch.

openssh, upstart, wncksync: This branch is in active use and appears to be constructed using a direct import of the upstream VCS. As a result, the upstream version tags are just "VERSION" not "upstream-VERSION", and the importer does not understand this well.

clutk: The karmic branch is importer-created. The lucid, maverick, natty and oneiric branches all have identical content, and are derived from upstream VCS. Unfortunately, they don't match what's actually packaged in the archive in any of these releases :-(. Therefore, I suggest backing up the existing branch, deleting them all, and letting the importer import from scratch.

The remainder all involve fairly straightforward errors of importing new upstream versions directly onto the packaging branch. In each case, my recommendation is that the erroneous revisions be removed from the branches, *along with tags pointing at them*, so that the importer can re-import them correctly - or just delete all the branches and restart in the cases where there is minimal history before the problem commits.

ldtp, accerciser, mago
mutter
open-vm-tools
python-oauth
xfce4-utils