I find this irritating. Put the ATU into bypass mode. Tune a few kHz and it goes out of bypass mode. I would not have designed it this way. Once it is put into bypass mode it should stay there until manually changed.
I don't have the MEM turned on and my 6300 does the same thing. I can be working split with the tuner on, if I just swap VFO's (both in same band) the tuner goes off and you have the do another tuning cycle. If it would just remember where it was at and just turn on that would be great. What am I missing here? Do I need to create a profile with the tuner on?