bug in auto-update in 3.8.3 and 3.9 breaks multisite child sites (public and admin)

[swordspres]

What gets broken:

• child sites show default hosting page.
• can't switch to any child sites in admin panel.

I have multisite on subdomains, each site redirects to its own domain through WordPress MU Domain Mapping.
I investigated the problem and it is not started with 3.9 but with 3.8.3 after an auto update: after having restored a previous full backup with 3.8.3 while everything was working, and having also added define( 'WP_AUTO_UPDATE_CORE', false ); in wp-config to avoid the auto update, in the night multisite was broken again. So i suspect that minor/security update on 3.8.3 broke my network (update released after 2014-04-18 18:23). Now i have restored again the same image (3.8.3) but added define( 'AUTOMATIC_UPDATER_DISABLED', true ); instead.
Any feedback is very appreciated as i have all my sites in this network.
I will check if it will work tomorrow with the define( 'AUTOMATIC_UPDATER_DISABLED', true ); rule in place.

EDIT: while obvious, i add that upgrading the broken install from 3.8.3 to 3.9 doesn't fix the problem.

[swordspres]

invalid: problem was due to nigthly auto update of cpanel/cloudlinux

[swordspres]

specifically, it became necessary to add domains to cpanel (addon domains) and point them to public html in order to resolve in the multisite network, while i never needed this extra step before.