Hi,
General system maintenance or deleting temp files is unlikely to affect working of the YubiKey because for the operating system YubiKey acts as a USB keyboard.
Based on the description it could be potentially related to the USB port on the computer since the YubiKey works on the other computer. Can you please try using it in another USB port on the same computer or connecting via a USB hub if available?
If the problem persists, please write to
support@yubico.com with the details about your hardware and operating system etc.