some observations:
without changing the First preset, i deleted blocks (replaced with Shunts) from the Second preset (saving, power cycling) seeing what needed to remain to keep the issue happening. it turned out Input, Flanger, and Output need to be in the Second preset, and need to have connectors between them.
once i found that, i then deleted blocks from the First preset. first i deleted the Synth from the First preset, and the issue didn't happen with an untouched Second preset. thinking it was the synth block causing it, i then made a new First preset that was just Synth to Output block, however, that didn't cause the issue.
so then i reloaded the First preset again, and tried deleting other things. it turns out leaving the Synth, Pitch and Out blocks with an untouched Second preset does cause the issue.
to isolate the issue, i then tried a new First preset with just Synth, Pitch, Output, and a new Second preset with just In, Flanger, Output. i expected the issue to happen, but something different happened: when changing to the new Second preset or the untouched 2nd preset there was only a "blip" of sound at Out 1 during the change, then it went away and everything seemed to be normal. this "blip" doesn't happen if you were on the Second preset on boot, then go to First, then back to Second, just like the original bug.
changing gears for a second:
i don't know how the First preset is supposed to work. there's a Pitch block that's Bypassed without auto-engage, with Mix set to 100% - meaning no sound gets through unless the Pitch is Engaged. if i Engage the pitch block, and put the Volume block Control to 100%, the level insanely clips. it's way too loud with this setup. it could be the +8 level in the Reverb block, it could be the Drive block. hard to say.
i originally thought that because the First preset is actually extremely loud, when changing presets, i think for a moment, the entire signal of the First preset is somehow "active" and causes the glitch.
however, i changed the First preset so that the Synth sound (the only input/source of the preset) wasn't loud with the Volume pedal fully up. the issue still happened after this change. i had to change the Level of the Synth to -43.9dB for it to be 0 on the Leveling Meter.
so the only things i could find are
the Input, Flanger, and Output blocks need to present in the Second preset with an untouched First preset.
keeping only the Synth, Pitch and Output blocks in the First preset (and an untouched Second preset) doesn't cause the level to go full, but causes a "blip" of sound at Output 1 - this blip vs fully clipped level is probably due to the other removed blocks in the First preset.
so it seems somehow "sound" or "data" is "continuing" through from the First preset when you change to the Second preset. an untouched First preset is extremely loud as-is with the Volume block set to full Control, and the Pitch block Engaged. i believe this is causing the uncontrollable nature of the originally reported issue.
however, with just Synth, Pitch and Output in the First preset, the uncontrollable nature of the issue doesn't happen anymore, but a sound does "blip" on preset change to an untouched 2nd preset.
from this, it may need someone who knows the internals to judge what's happening with those observations. for convenience, i'm attaching the "new" presets i mentioned earlier - First X is just Synth, Pitch and Output, Second X is just In 1, Flanger, Out 1. trying these out, booting with First X active, then changing to Second X, you should see Out 1 meters jump up a bit on preset change.
btw, i rebooted about 50 times or so, each taking 20 seconds, and it didn't bother me at all.
)