I have been having problems with WordPress Updates for a while. No error messages, just the WordPress Update, or WordPress Plugin Update, hangs.
Then I found out that the WordPress backup plugin I am using, BackWPUp, failed if I configured it to use any compression.
Then I found out that the problems I had been having with random-seeming 500 Server Errors was from the WP-Super-Cache plugin configured with, hmm, compression.
WordPress Updates would create new folders, but no files in them.
I wrote a PHP program, outside of WordPress, to test if the problem was in WordPress, or in the version of PHP used on my server.
The problem is in PHP. The PHP unzip routines lock up. No error message on screen, in the PHP log, or in the system log.
WordPress 3.6.0 and 3.6.1, Multi-Site, Apache, PHP Version 5.2.17, [HTTP_ACCEPT_ENCODING] => gzip, deflate
PHP itself has a bug in Zip/Unzip in old versions. Hangs without any error message displayed or in logs. Affects WordPress Update, and Plugin/Theme Updates, and any plugins that use compression (e.g. WP-Super-Cache or BackWPup)
PHP Change Log http://www.php.net/ChangeLog-5.php#5.3.4 says
PHP Version 5.3.4 released 09-Dec-2010 – Fixed crash in zip extract method
Note: PHP versions are numbered so version 5.3.10 is higher than 5.3.9 (5.3.1 is lower)