Hello,
I have the BeatStep Pro by a few days and my Sub Phatty is a month old, so I'm not an experienced user, but I try to help you anyway.
Did you check values of the randomness/probability knobs?
If these are zero, have you tried connecting the BSP directly to the Phatty via MIDI din and/or with another patch?
Is the behavior the same?
Maybe the patch has some modulation settings that cause the problem in combination with gate/velocity settings on the sequencer.
Try a patch "from scratch" (Active Panel + Initialize Preset).
I haven't Cubase so I can't help you on that.
Let me know.