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I would refer you back to post #2 for the most likely causes. The fact that Ike was able to tun the upgrade suggests that whatever was at play is either (a) Not being actioned on every ajax call - or (b) only run for specific users. Maybe one of those rings a bell...

As to upgrading to 5.6.3.1 then I would recommend it. If it fails for you as a forum admin, try it with another account that isn't one. if it still fails then we can tell you the data change to make in the database which is very simple through a tool like phpMyAdmin probably available in your hosting console.

And the most usual way to find the suspect is to deactivate other plugins until the culprit is found which then makes it easier to diagnose. By the way - if you have any sort of chat plugin active then that really SI worth deactivating while you upgrade.