Getting Automatic WordPress Updates To Work

Hello,

I have been trying to get automatic updates to work. I’ve done a lot of twinking and a lot more waiting for the wished-for updates (supposedly they happen only at 7 AM/7 PM local time). So far only one domain installed automatically out of 15. Not sure what makes it different other than the fact that a certain security plugin (Acunetix WP Security) isn’t installed on that domain.

Here is my current setup:

Server: LEMP on Ubuntu 12.04
Server Security: OSSEC – a factor?
Wordpress: running 3.9 on 15 domains

Subversion was previously used to update WordPress. However I recently uninstalled it and manually removed all subversion folders.

I tested the Background Update Tester on all domains and passed with flying colors for the most part. Only one domain briefly said it had problems getting check sum then it reported all good results for automatic updates when I refreshed the page.

I added these filters to wp-config just in case subversion is _still_ detected:
add_filter( 'automatic_updates_is_vcs_checkout', '__return_false', 1 );

Also added this to update themes:
add_filter( 'auto_update_theme', '__return_true' );

Still nothing. Nada. No email about updates to 3.9.1 I still get begged to update when visiting the wordpress admin pages. What can I do differently? And is there a better way to know updates _will_ work other than waiting another 12-24 hours?

Edit: Maybe it is the security plugin. Just wondering if anyone has same issue. I would hate to disable it.