I have the same problem. Started to show up after I created various logbooks to try and organize my flight times for different aircraft. Never figured out why it happened or how to fix it though which is a bummer. The message would go away if I selected a specific log book during flight, but nothing would get logged even though the prompt would come up after I exited the session.
Now I just log all time manually right after I touch down. If anyone figures out how to fix it I'd like to know also.