I had intended to try this out for a while now, SpaceJam.  I went as far as nearly duplicating your MIDI assignment screens in H9 Control, and MIDI ‘Learned a CC #44 to Looper – Flip Direction in the H9 itself.

I’m sending CC messages with an FCB-1010.  Various static values using the footswitches; performing as expected.  Continuous values of CC #44 via footpedal stuttered the loop until the values settled down.  Also expected: the Looper is trying to incrementally flip directions under a barrage of MIDI CC values.

I don’t see anything wrong in your MIDI assignment images.  On the off chance that the LF Mini was sending MSB / LSB MIDI CC’s, I thought there might have been a CC #16 “clue” somewhere.  This is baffling …  I can’t reproduce the issue.  Have you used a MIDI monitor to check if the LF Mini is sending anything else unusual?