Still very hard to track down (now entries in the server / apache error logs) but it seems like there would be still a file lock on latest.zip when the piwik Updater tries to access it. File is in the given directory, permissions, etc. are correct.
Error was reproducible on my 2 Servers (which have the same config (basepath restriction, vhost, mod_php (5.2.6)). AutoUpdates used to run correctly by now.
Bug related to #1965.
Tracking down the error more deeply:
Is that your fix?
Ok, it is a patch. I'll apply and close.
My fix was to replace the Plugin "CoreUpdater", "/core/Unzip.php", "/core/Unzip/PclZip.php" and "/core/Unzip/ZipArchive.php" with the new files from 1.2.
The patch file fixes a warning (and that a possibly existing tmp/piwik directory is correctly removed) in "plugins/CoreUpdater/Controller.php" that uses "file_exists($this->pathRootExtractedPiwik)" while the member "pathRootExtractedPiwik" wasn't set yet.