I did have issues one time where I accidentally grabbed the wrong color piece when laying out my moves. Everything I did after that showed up correctly at the time, but when I looked back over the sequence later, everything from that point on was corrupt and weird. I don't know what would have happened if I hadn't caught that and deleted the corrupt sequence, but it could have been ugly.
Conditional moves
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Has anybody had issues with conditional moves auto playing moves that are different that the ones you selected?