A while back I was playing Half-life on Steam, and every so often a classical madrigal would start playing, with oddly familiar voices. A truly strange bug; I couldn't think of any good reason for it.
Months later, I opened my computer's DVD drive for once, and discovered the reason: my sister, a professional classical singer, had sent me one of her recordings, and I had put it in the computer to listen and forgotten about it for the next year.
Somehow the game was--from its original on-cd release--assuming the proper soundtrack was on track N of the CD, instead of the Steam install.
Remarkably simple in the end, but a very baffling bug at first.