So I have a few WordPress sites running on my VPS (Ubuntu 12.10, Nginx, php-fpm 5.4)

The sites are all on seperate vhosts and use their own config files (albeit similar to each other) and vary in complexity. One is very simple and uses minimal plugins.

When I try to update core on any site via the admin area I click the "Update Now" button (which should run the script in wp-admin/update-core.php the page hangs for a minute or two before going to a blank admin page (i.e. the wp-admin menu bars and header bar are there but there is no content in the body of the page). Visiting another admin page via the still menu bar reveals that the core has not been updated.

Checking the error log I see this entry:

2013/10/29 23:20:48 [error] 9384#0: *5318248 upstream timed out (110: Connection timed out) while reading upstream, client: --.---.--.---, server: www.mysite.com, request: "POST /wp-admin/update-core.php?action=do-core-upgrade HTTP/1.1", upstream: "fastcgi://unix:/var/run/php5-fpm.sock:", host: "mysite.com", referrer: "http://mysite.com/wp-admin/update-core.php"

This didn't happen in the past on older updates and the rest of the site including updating plugins works fine.

Any ideas? Could it be as simple as a time-out error? I find that unlikely as the server should munch though a wp upgrade in seconds.