I am not sure if it is related but I had issues too. I updated from 2014 to 2101. The update works fine and the proper version is showing on the status page, unlike for the OP of this topic.
However, there seems to be an issue with the Navdata. In my case, I am trying to do a flight from YBSU to YSSY. The routing according to Simbrief gets me out of runway 31 via the MOLOO SID. Both, runway 31 and the MOLOO SID are published in the Jeppesen charts (also those coming with Navigraph) and in the official charts of Australian Air Service. However, in the MCDU Flight Plan, when I select a departure, I can only select between runway 18 and 36. Neither of them exist and neither of them has a SID or STAR. It seems that 18 / 36 refer to a short second runway, that has been decommissioned.
The weird thing is, that upon checking the CIPF folder and in their YBSU, I can see that in the file there is runway 31 and the MOLOO SID in there. That leads me to think, that either the AIRAC is not update completely or not read properly by the aircraft.