If rawcount counts up and down, but the DRO is wrong, then you likely have a scaling problem.
1.1. Voltage Checks
The A pair and the B pair should behave identically , that is all pins should have roughly TTL level swings (with a 0-.4V low and a 2.4 to 5V high)depending on shaft position if the A and B pairs behave differently I would check your wiring.
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