Piston behavior is not consistent. I know that's not descriptive, so I've included the machine I was building when I found this. The behavior of the pistons seems to change depending on where it is in the world. In addition, the behavior of the pistons in each row is not consistent. Just pull the lever at the end of the repeater track and you'll see what I mean. (the lever down the bottom corner resets all the pistons) I'd post screenshots, but the pistons are surrounded by wires, so you can only see 1/2 of them at any given time.