FYI, I committed the rp2040 Kconfig settings to the master Klipper branch.
That doesn’t occur for me, but it doesn’t sound like it is related to the micro-controller type. Sounds like something odd at the OS or USB wiring level.
Last I looked there was just the two adafruit boards that used generic_03h (at least as defined in the pico sdk). I’d guess those two boards aren’t particularly common, but if you’ve got a better way to describe it in Klipper then feel free to submit a PR.