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I have the same scanners though and have connected the galvo signal inputs to the ground.
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We recommend a ground free operation between computer and drivers
Just because you can connect them doesn't mean you should. The only reason you should tie grounds together is if you're using the ground as a signal reference. In the case of those galvos, the ground input on the signal port of the galvo drivers serves no signal purpose as only the differential pairs are used for position input.
If you connect the grounds, all you'll end up doing is creating ground loops as the ground hops from the galvo PSU, to the galvo driver, to the signal ground, to the other galvo driver, and back to the PSU. You don't want that, as it'll soon be picking up a 50hz/60hz signal from the power mains, causing the wavy distortion that OP is seeing. Sometimes you can't avoid ground loops, but this kind of ground loop is completely avoidable and unnecessary.
^Listen to the man..