When I upgrade Magento from 18.104.22.168 to anything over 1.9.3 (using Mage_All_Latest), everything seems to go alright until the cache is cleaned. As this loads the entire Magento core, all necessary upgrade scripts are ran, and in this case it starts running upgrade scripts from ancient versions leading to MySQL-exceptions about existing tables etc. The same happens when trying to access the admin panel or the actual shop website.
Upgrading to 1.9.2 works fine, upgrading to 1.9.3 from there on (after fixing all the OpenSSL dependency bugs in Magento Connect) gives the same result again.
Another thing I noticed is that while the downloader reports the correct current version at the bottom of the screen, the current versions of all the packages are stuck at 22.214.171.124 even after they've been (successfully) upgraded to 1.9.2.x.
The server is Centos 7 with ISPConfig setup.
Of course I'd love to know the cause of this problem but I'd settle for a way to force the correct version numbers somewhere somehow to stop the upgrade scripts from running amok.