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Differential signaling is more resistant to EMI generating false step/dir signals
but where there is enough EMI to actually damage components, a single ended
connection is more resistant to damage since common mode EMI (applied to both
+ and - signals) is mostly eliminated.

Single ended connections would be:

7I96S GND      DRIVE PUL-, DIR-
7I96S STEP+   DRIVE PUL+
7I96S DIR+     DRIVE DIR+

 

Is there some other device you can ping to see if the issue is the host or the FPGA card?

Le acabo de poner una pica de tierra al lado de la pata de la mesa en la parte de atras para tener tierra totalmente separada.

Me puedes confirmar lo de single ended.

Gracias