Probably nothing that I am not missing as well. 
Prior to SU12, there were always times where ATC did not (at first) use the callsign I had put in MSFS as my default, but then, later, ATC would magically switch to using that callsign.
The Callsign label on the Plane’s Panel was always correct – ie what I had put into MSFS as my default Callsign.
Now, since SU12, what ATC seems more often to Ignore my set MSFS callsign, and use the callsign in the plane’s config file, sometimes never changing to my MSFS personal set default.
A definite change & degradation in SU12
Hopefully, now these callsign issues have got worse, Asobo may take a look at this and make a permanent fix, including looking at Tailnumbers being passed over to planes in Multiplayer, and displayed on the plane.