What I have learned while using motor control workbench: Encoder and motor are synchronized when start button is pressed first time.  Status is "alignment" during alignment in motor pilot. It will do it only once after boot Motor movement should not ...

Have you tried to switch encoder A and B wires? Encoder rotation direction should match motor rotation direction.

There is no ui for position control.Position control example in "MC_SDK_5.Y.1\Projects\NUCLEO-F303RE\Demonstration\PositionControl\Src\main.c".

Motor control workbench -> Digital I/O -> Encoder interface -> Timer= TIM4 CH1=B6 CH2=B7