Hi Patrick, this should all be consistent within MIDI Designer, but we'll test for that too. First though, we'll investigate the most likely suspect, which is the MIDI Designer layout. Can you get a MIDI Monitor on your output somehow? Best would be on the computer, for instance. The supercontrol chain, once fired, goes to the end, even if the original control is deleted (you'd have to be fast). So... what's different about that chain? It could have the subs in a different order, etc. (they can be ordered, that's the edit button). Check out the output in a MIDI Monitor and let's investigate further, please.
Or go the other way: delete and recreate. Might save time but we wouldn't know the cause. I'd say: recreate and don't delete. That way we can see if it happens the second time, and have a "control" if the new one works.