This might be a jackd thing, but it seems like a Pd thing. Running 0.39-2 as provided by Debian GNU/Linux. When I select 3 inputs and 1 outputs for Pd's MIDI, it shows in the Jack control panel as 1 input and 3 outputs. Is this known? I wasn't sure whether to make a bug report because I honestly don't know what program's causing it.
-Chuckk