Yes, it drives me crazy. I sit there out in the field or on a river bank, wondering who is watching me perform some incantation on the remote as I wave it on the horizontal figure 8. I also am not entirely clear if I am doing the motion correctly.
4/5 times this has happened, it never goes away. I just end up cancelling it.
One time, I did not even do the motion, just picked up the remote and started walking to distance myself from the parking lot and then it suddenly chimed and a "Calibration successful" message appeared with an OK button on the remote in place of the instructions.
Seems silly. Theory above is very good one: Perhaps the remote relies on the Phantom's compass and forces calibration when the drone is not connected. Maybe that one time I started walking I had just turned it on and it happened to connect at that moment.