@Nathan Navarro Okay. I did a lot of testing last night and there are so many variables that it's really hard to narrow things down and draw conclusions, but I'll try to make this as simple as possible by clearly stating what are facts/observations and what I'm concluding from those facts/observations.
PREVIOUSLY DETERMINED
(1) Under certain conditions, my SB2 pedals jump to different settings---seen in the Vine above.
(2) Through previous examination with the Hub Manager, it appeared that the settings the pedals were jumping to were the settings stored in Scene 0 of the Hub.
(3) My kludge to override this was that make Scene 0 of the Hub "null." Though inconvenient, this worked well enough. But it sacrifices more than a scene; with the Hub constantly jumping to the null Scene 0, my settings don't change, but if I try to save a scene from the Hub directly it will only save to Scene 0.
OBSERVATIONS FROM LAST NIGHT
I'm only going to discuss what I clearly observed last night. I feel like it's possible I've occasionally seen exceptions to the behavior below, but for simplicity I won't include any of that.
(1) I was able to clearly correlate the jumping/settings changes with being hooked up to the Beat Buddy. I plugged (by MIDI) the Beat Buddy straight into the Hub and got the behavior. When I unplugged the MIDI cables OR set the Beat Buddy to "Thru" instead of "Out," so that that the Beat Buddy should not be sending any data, the jumping stopped.
(2) I tested what was coming from the Beat Buddy with a M-Audio UNO interface into my laptop and a MIDI Monitor program. When the Beat Buddy is not playing, nothing shows up. When the Beat Buddy is playing, there is a series of MIDI Note On and Note Off messages. Apparently MIDI clock and any real-time messages are not picked up by this monitoring program I was using.
(3) I tried the same thing on MIDI Designer on my iPad and saw the same messages.
(4) I tested the MIDI Monitor program on my laptop just to make sure it saw PC and CC messages and it did.
(5) The M-Audio UNO does not do MIDI Thru by default. When hooked up to the MIDI Monitor program (it's literally called "MIDI Monitor"), I can set it to Thru. This actually influences the behavior of the jumping on the Hub. When hooked up directly to the Beat Buddy, the Hub will jump scenes regardless of whether the Beat Buddy is playing or not. When hooked up with the laptop and set to MIDI Thru, the Hub only jumped when the Beat Buddy was playing (when MIDI Note On/Note Off is being sent), not when it was stopped (when the monitoring program is not picking up anything, but I assume MIDI Beat Clock is still being sent).
(6) I tried various states of "filtering" on the MIDI Monitor program (i.e., filtering out various types of messages), none of which had any influence on the behavior of the Hub. But to be clear I'm not really sure how the monitoring program or its filtering works.
CONCLUSIONS
(1) To the best of my knowledge and experimentation, the Hub is jumping to Scene 0 without any PC or CC messages being sent.
(2) It is slightly ambiguous whether or not the Hub jumps scenes due to MIDI Note On or Note Off messages, because the behavior is different when the monitor is in line. But the monitor says there are none of these messages when the Beat Buddy is stopped, and the Hub will still jump when the Beat Buddy is stopped and directly connected to the Hub.
(3) It is further unclear what other messages the Beat Buddy is sending in its stopped state (I know it is sending MIDI Beat Clock if nothing else).
TL;DR
The Hub is definitely jumping due to something from the Beat Buddy, but the Beat Buddy is not sending a PC 0 message as far as I can tell, which is what the Hub is interpreting.
@gastric - do you have a Mac-based MIDI monitoring program that you recommend?
Thank you very much for taking the time to put this all together. Because I'm unable to replicate your problem with other midi clock devices, we've ordered a BeatBuddy and will try again when it arrives later this week. I feel you on losing your presets, it happened to me once with my M9, and I know it can be a huge headache. I recommend keeping backups secured in a dropbox folder, or something similar and internet-based, so you can access it if need be. The "Erase All Scenes" option in the HUB Manager is essentially the hard reset for the HUB. I look forward to getting to the bottom of this and getting your awesome board working as it should.