I don’t have an answer for you but I do have some questions, based on your troubleshooting:
Was it working before you flashed the firmware?
Why did you use the QMK tool instead of CORE to flash it?
Did you flash it via your laptop or your desktop?
Have you tried reverting to CORE instead of QMK?
Have you tried using motherboard ports instead of the front panel?
It’s super odd, it feels like something might be conflicting with the firmware on your desktop. Let us know if you hear back from support.