You replaced the controller and it still does it? Whoa, that's weird. I'd immediately suspect the voltage reaching the controller/steps. What it sounds like is a bad or dirty connection somewhere causing the controller to go all wacky. Maybe early in the supply wiring where there's some corrosion or a bad relay or even a rare intermittent fuse. The motor draw causes the voltage to dip, that resets the controller, rinse and repeat.
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