You mention you're running under Linux. Do you see any new lines in dmesg when you plug it in?
Honestly, if it works in bootloader but not in normal mode, it could be firmware. Are you totally sure you've got an up to date firmware designed for a Pico on there? The bootloader won't stop you flashing (for instance) an Original Espruino firmware on there, in which case you'd see exactly this problem.
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