Hi Jan,
I didn't find a solution with the GeoEvent Server. To solve the problem I had to develop my own Windows Service which posts data directly to the Big Data Store, circumventing the GeoEvent Server altogether. I find the GeoEvent Server rather buggy and unpredictable.
My dataflow is pretty simply, just XML files transformed to JSON and posted to the BDS. As I can't replicate the bug using the simulator, my guess is that the problem in my setting occurs when I have a number of threads posting data to GeoEvent Server simultaneously.
Regards,
Bjarke