It might be a hardware failure, especially if the machine is a bit old.
Or some cables could be loosely connected, check them too. Or the connector might be slightly broken, since it sometimes work.
When you boot with the USB installer stick, do all USB ports work properly? If so, then an update might have broken something.
One thing to check is the BIOS/firmware, is it up to date?
I experience the same problem. USB ports are detected when booting live from USB, but no USB device detected by the OS when logged in.
EDIT: sorry, to soon. Reinstalling the linux-firmware and linux-headers and rebooting the system fixed it. Thanks.