When I’ve run into “thunder” or “squealing” conditions that build up over time, it’s been due to a high feedback / recirculation setting. When pitch shifting is inside the feedback loop routing, it can shift higher (or lower) each time it travels around the circuit. Eventually, the signal will reach the upper / lower limits of the device bandwidth, and continue to circulate. It can also happen with a little noise or hum in the signal chain that gets fed back, and builds up gradually.
I’m not saying that’s what’s happening here to everyone, but it’s one thing to look into. The Feedback / Echo Level parameter doesn’t have to be 100-110 for this to happen. Depending on the algorithm and related parameters, sometimes it can be set as low as 90, or 85. In my high-feedback looping presets, I’ll program a HotSwitch or expression pedal to “reset” the Feedback loop to low values, and then back up again where I want it.
It’s a good compromise for balancing the high regeneration levels that I need from the preset, and the tendency / potential to build up unwanted artifacts over time.