It typically happens when I'm in the middle of something and don't have time to experiment. My setup is using only visual metronome via the icon. Haven't checked against screen-flash or audible click. I use it mostly for songs where I play an intro and thus set the tempo. I don't want an audible metronome on stage, and a flashing screen is terribly distracting when it is out of sync with the band. I have tried to only have the count-in running for a number of bars, but find it more flexible to have the icon flashing all the time and just ignore it when it is out of sync.
Sometimes the icon-flash is simply wrong, but stable. Other times it is irratic, as if the beats from two songs are put on top of each other.