I'm not necessarily the most experienced with this issue, but it really sounds like an issue tied to your database. Have you tried to do a recovery to a point in time where that issue was not occurring? This is why it's really necessary to constantly back-up data. Sometimes databases have hiccups much like the one you are currently experiencing.
Again I am no expert, but that would be the first thing I'd think to check. - Wait till someone who is a 'someone' on WebFlake gives you a response.