I maintain the pi3d package which is available on pypi.python.org. Prior to v2.8 the latest version was always returned by a search for 'pi3d'. Subsequently v2.7 + v2.8 then v2.7 + v2.8 + v2.9 were listed. These three are still listed even though I am now at v2.10. i.e. the latest version is NOT listed and it requires sharp eyes to spot the text on the v2.9 page saying it's not the latest version!
NB all old versions are marked as 'hidden' I have tried lots of different permutations of hiding and unhiding releases, updating releases, switching on and off autohide old releases, editing the text of each release etc ad infinitum.
Is there some obvious cause of this behaviour that I have missed?
Upon searching pypi.python.org for pi3d I have found that when you go to the pi3d v2.9 page there is now a large bold warning saying that it isn't the latest version and gives a link to v2.10 which was probably put there between the time you asked this question and now. However the fact that the v2.10 was not listed for me shows that your problem is not a local one. Googling site:pypi.python.org pi3d shows pi3d v2.10 as the first result which means that something is wrong with the pypi search engine.
The answer to your question is no, there is not an obvious cause of that behaviour. The fact that when I use Google I get a result as opposed to the builtin search implies that their search backend needs to be reindexed.
on pypi.python.org what would cause hidden old versions to be returned by explicit search