Without doing an intensive investigation into what you're doing(don't ask, my background is even more intensive), it's hard to say exactly what is going on.
First off, it's easiest to train MyDMX via note on commands, but you know that, apparently. Excuse my ignorance, there are so many MIDI devices that I do not know much about what the Roland FC200 can or can not do or handle.
Obviously, you're having success with MyDMX and MIDI triggering. But, live as a real musician, it ain't working so hot. I hear ya. But at least we understand that you have your signal flow happening right.
When training MyDMX, you want to keep things as SIMPLE and CLEAN as possible. Why? MyDMX will take the first thing thrown at it when "learning". I know, not ideal, but really, that's how it SHOULD work. Only send it what you want it to learn. If you're sending a stream, it doesn't know good from bad. So, if that "listen" screen is vanishing right away, yeah, you've got some sort of continuous controller(please, not CC) data going on and that needs to be STOPPED at least for training/programming/learning purposes. MTC uses different information, albeit in the same data stream, but it is uniquely identified. If something is using that to listen for a MIDI trigger, that's what we would call BAD. Do have MyDMX do this would require a deliberate effort on the programmers to violate accepted MIDI specs and norms and I doubt they'd make that type of extra effort.
Your isolate mentality is playing in your favor. It appear sit would be your keyboard generating all sorts of lovely fun stuff that you don't necessarily want. What I must ask is what are you doing with this keyboard? Is it a sound module/source? Is is a performance unit? I've seen tours with stacks of keyboards not played but used as sound modules because there is no rack equivalent. Ideally, continuous controller data should only be loaded when the data is being used. Such as a pitch bend wheel or portamento or after touch, things like that, when not in use, "go silent"
Is the keyboard also a sequencer? If so, is there a valid reason why it is sending MTC? If you're triggering tempo-controller drum loops, then MTC should be used, but otherwise, you should just hard sequence the drum stuff, assuming an external drum unit. Unless something has to lock to that MTC source(again, assuming MTC), why the hell are you doing that on stage? That's suicide. It's best to just do it right and direct call it.
But, I don't think you're sending MTC all the time. MTC usually isn't sent when no sequencing or say, SMTPE chasing is stopped.
What I'd do is dive into that keyboard and see why it's generating so much traffic. once that's done, I think you're probably 95% of the way there, if not 100%. It points at your keyboard based on your troubleshooting. Start there.
If you don't resolve the issue with the keyboard, it won't matter what foot controller you buy. Or if anything, train MyDMX with the keyboard not plugged in and see what happens with your foot controller when it sends data. Most foot controller sent patch change type data, but I would think MyDMX would respond to such commands. Just make sure nothing else is using that channel on that MIDI port, which is probably something you've already addressed anyways.