Analogue-sequencer

Very weird problem.
My first thought was that the merger should only be accepting midi clock
from one input. Depending on how it decides to switch between which input is
active for clock, you may not always have clock passing through the merger
as you expect.
Assuming that's not the case, have you tested whether notes are passing
through P3 OK ?
Is it actually receiving anything from the merger ?

Cheers,
Colin f