Turns out the problem wasn't fixed.. I took a closer look, it was spitting out a lot of errors in the console... I restarted it and the problem continued...
After looking at the permissions the problem became obvious - they were all wrong - root was the owner instead of the user running mta, so I've changed the owner and the errors have gone from the console.. re-entered game and it's now recording stats properly again.
There was no damage done to the actual statistics because the root problem was it couldn't write/save to the database... now it can.
It would have been nice if someone could have told me there was still a problem... I was under the impression that it was all fixed.