The code worked differently when the moon was full
We once had a customer who would call us in a panic a couple of times a year saying our inspection equipment was experiencing unusually high false rejects and they were generating very high scrap rate. By the time we got a technician on site the next day, everything was working flawlessly and the customer couldn't reproduce the problem either. This went on for almost three years with various levels of escalation to the current management. Finally, one day a technician was on site for another project when the customer came up to him and said "It's happening right now! Come fix it!" The technician rushed over to the equipment and discovered that the sun was shining at exactly the right angle to cause a lens flare in one of our cameras. This happened twice a year as the sun moved along its trajectory. A strategically placed piece of opaque plastic fixed it permanently.