That's puzzling. I run a Sonar or Lexicon MPX-1 MIDI Clock through a PitchFactor -> H9 -> MIDI Thru -> ADR III & EHX 8 Step Program. I thought your problem might be one of the MIDI -> CLK OUT set to On, but it doesn't seem to affect pass-through of the MIDI Clock (with MIDI -> OUTPUT set to THRU).
I also tried toggling the MIDI -> CLK IN settings to OFF, but again, the downstream clocking didn't seem to be affected. (Of course, the local device doesn't track the MIDI Clock in that scenario). I connect the live rig to the studio operations through a MIDI router, so let me double-check my findings for any missed Merge routings.
FWIW, the newer PF firmware flashes "CLK IN" when it's not receiving MIDI Clock. That may help with diagnostics. I haven't seen that feature in the H9. MIDI Channel setting won't affect Clock. MIDI BPM seems to update very quickly on the Eventide displays with newer software revisions. I've never had to mess with the CLK FLT position, but that's about all I can think of that's left.