Hi,
I have solved this issue.
This might help other shaving similar issues.
The problem in my case was that one of my grok fields is: _timestamp, which just happens to be a metadata keyword in elastic, so it barfed every time it saw it, thus stopping that and all other fields from being indexed, but not always stopping the event from being stored (with the default fields that were already there).
So always make sure all your fields are unique and reserved.