This is kind of something that shouldn't happen, but it might be necessary to check also the release date/time of dists while calculating is_latest.
http://search.cpan.org/~rizen/Task-WebGUI-2.0000/ (13 Dec 2011)
http://search.cpan.org/~colink/Task-WebGUI-2.0000/ (27 Jun 2012)
See also charsbar#14
can you just look at what PAUSE says is indexed?
(for stable releases, it's the first (chronologically) release with that version; for dev releases, it's the last.)
That's probably not enough, as we are also analyzing backpan distributions (in this case, both are still on the CPAN, but that's not always true). I'm experimenting with 06perms locally, but it's going to take more time to settle.