One of my favorite mysterious test failure is from BeOS folklore:
http://www.haiku-os.org/legacy-docs/benewsletter/Issue4-22.h...
A Testing Fairy Tale
Two test engineers were in a crunch. The floppy drive they were currently testing would work all day while they ran a variety of stress tests, but the exact same tests would run for only eight hours at night. After a few days of double-checking the hardware, the testing procedure, and the recording devices, they decided to stay the night and watch what happened. For eight hours they stared at the floppy drive and drank espresso. The long dark night slowly turned into day and the sun shone in the window. The angled sunlight triggered the write-protection mechanism, which caused a write failure. A new casing was designed and the problem was solved. Who knew?