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It turns out that this error may be a problem with MoveIt itself. I tried my code on many different test cases and it worked properly (gave correct times between points and moved the arm) some of the time, after I tried quite a few paths. It seems that when MoveIt cannot find a proper path in some cases, the success boolean may still be true, but the waypoints still might all have time from start of 0, and the path can't be executed.