Your M5 can serve as a simple midi device, for future trouble shooting/programming.Well, that's all pretty reasonable and it's my next step (I didn't have a chance to troubleshoot last night, I will tonight).
However, there are a few problems with it. One is that I don't have a "simple" MIDI controller, by which I take it you mean something like a MIDI Mouse or One Control Gecko. So I can't change scenes without connecting a device (laptop, iPad, or Android device---I could do any of the above). This limits how well I can isolate the variables you are talking about, although I can still isolate things up to a point.
A lesser problem, and not so much a problem per se, is that in theory I should know when my iPad/MIDI Designer/M-Audio UNO setup is sending MIDI data. Lights blink when data is being sent---on both the app and the interface. Even though there seems to be a correlation between what is hooked up and the problems, there doesn't seem to be a correlation between what MIDI data I've tried to send (or when I'm sending it---there is not continuous data being sent from the iPad) and the problems. Furthermore, I've had pretty much perfect success with this setup and all of my other pedals. So while I agree it's something I should test---it wouldn't be scientific if I didn't---that explanation doesn't seem as likely to me as it seems it might be to the rest of you.
Sometimes I feel like a creep for knowing forum members boards as well as I know my own. But then I remember I own most of my pedals because of rave reviews from those same forum members.