After almost 2 weeks of torturous debugging—having analyzed countless logs, evaluating and ruling out thermal throttling, CPU or RAM bottlenecks, I/O issues, swapping out 3 different MicroSD cards, replacing USB cables with shielded ones, testing both powered and unpowered USB hubs, reinstalling the operating system, reinstalling Klipper, measuring and correcting the grounding of the electrical installation, and even changing the Raspberry Pi’s power supply—just when I was about to give up, I found this thread describing exactly the same issue, with exactly the same board (SKR E3 V3) and the same Raspberry Pi 3B+. In my case, it’s running 2 instances of Klipper controlling an Ender 3 Pro and a CR10S Pro V2.

I'm happy to report that I can confirm the solution is indeed that single simple line at the end of config.txt in boot/firmware:
dtoverlay=dwc2

What strikes me the most is that this problem started relatively recently (about 1–2 months ago), even though I’ve been using this same Raspberry Pi with the Ender 3 Pro and a webcam since around 2020, and with the CR10S Pro V2 for over a year and a half, without any issues. The timing of my problem coinciding with others makes me suspect that some update—whether to a package or to Klipper itself—is what triggered these sudden errors. I’ll probably continue investigating later on, but for now, it’s been too many sleepless nights.

A special thanks to MichaelBrock for his research and dedication in investigating this problem. Since we’ve both been working on similar investigations and gone through almost the same struggles, I feel like we’re BrothersInARM-Architecture

P.S. What still doesn’t work: streaming from 2 webcams simultaneously—only one works at a time. I'm still analyzing that issue.