Any 'news' on this? I still have this problem. I suppose it is still on the 'to fix' list Dave? Or maybe you have already fixed it! (How near are we to the next update BTW?).
I noticed something else that shows that there is an oddity here. Even though I am in Mode 2, when ATC either says 'Maintain heading xxx', or 'Maintain current heading', there is never any acknowledgement from the pilot. All other instructions from ATC get a response in Mode 2.
For now, I try to remember to use Dan's workaround, and request clearance at pilot's discretion. If I forget, then I get no more from ATC (as reported originally). When I land, I get 'clear to land' confirmation and so on... PF3 catches up and will after a while recognise I am on the ground. If you need another log, I can upload it.
Martin