Currently if I do an upgrade over the web, everything works ok until the 'upgadesettings.php' stage, where I get:

Site is being upgraded, please retry later.

Debug info: 

Error code: upgraderunning

Stack trace:

    •    line 476 of /lib/setuplib.php: moodle_exception thrown

    •    line 574 of /lib/setup.php: call to print_error()

    •    line 107 of /config.php: call to require_once()

    •    line 26 of /admin/purgecaches.php: call to require_once()

I can reproduce this consistently by manually reseting my main version number in databsae and running the upgrade.

1. update mdl_config set value = '2013050700' where name = 'version';
2. Hit https://dan.moodle.local/integration/admin/index.php?confirmupgrade=1&confirmrelease=1&confirmplugincheck=1
3. Goes through the 'system' upgrade successfully
4. Next page redirects to upgradesettings.php where i'm locked out.

It resolves itself after a few minutes, Eloy has discovered thats because upgraderunning is expired after 300 seconds by default.