It looks like logic is the issue here. All worked as expected in ableton. I'll keep messing around and see if I can come up with anything.

@gsagostinho I'm on OS X 10.10. And I mean two different instruments within logic. So two tracks, each set to receive midi for track 1 on channel 1, track 2 on channel 2.

Thanks for the quick reply.

So I've been using IAC and noteout objects to send midi values to logic. The only problem is even when I have the output channel in PD set, [noteout channelnumber], and the input channel set in logic to the same value, the values are still either sent or received on all channels. I've tested this via a very simple setup sending a note to channel 1, and a note to channel 2, with 2 different software instruments set to the right channels, but whenever any midi value is sent, it still arrives at both instruments. Anybody have any ideas as to why this is happening? (And yes, I have auto demix for multitrack already checked). I'm pretty new to this area in general, so it's possible there's something I'm not understanding about the setup.