Hi NeoTo,
I experience exactly the same effect, but with an Smoothstepper USB. If the encoder of the pendant, based on the PoKeys56U, for SRO at pins 5 and 6 is disabled, there are absolutely no problems with the smoothstepper. The fault with the smoothstepper, as mentioned by TanTan, occurs only with the encoder for SRO set active, even with RC- filters attached to the inputs. There is no difference whether you make a move of an axis with the MPG or by running a job.
With the spindle switched off, it doesn't matter whether the encoder for SRO is active or not.
Wolfgang