Not so much a software bug, but back in my early days (late 1990s) supporting an office network in London there was a computer where the mouse was making the cursor behave erratically during roughly the same period every afternoon. We swapped out the mouse, the controller card, even the computer - effectively replacing all the physical equipment - and nothing seemed to stop it. We went through all sorts of ideas - too near the microwave, heavy fax machine usage, someone's mobile phone - until we realised that it was optical mouse, and the sun would shine through that window each afternoon at the same time and screw up the sensor in the mouse. We stuck a bit of cardboard to the side of the desk and it never happened again.