try this, switch php branch from whatever you are using to different branch, update, switch it back, update.
(Example: 5.3 to 5.4 update. 5.4 back to 5.3 update)
Change php type to ruid2 or itk, then back to php-fpm (assuming you are using php-fpm). Update each time.
(Example: php-fpm event to ruid2 update, ruid2 back to php-fpm event update)
SSH:
sh /script/restart-all
Should work after that, old trick.