Hi Alan
I have this occur on some files too. A couple of workarounds worth trying.
1) Hit the footswitch in the middle of a bar, instead of trying to synchronise it . It won't change until the start of the next bar anyway.
2) Hit either of the fill buttons,or footswitch controls to same, and imediatly afterwards hit next panel memory button. or footwitch WHILE THE FILL IS STILL PLAYING. Both these work for me on the odd file that this glitch occurs on.
Good luck .
Eddie