I've noticed this as well. It seems that when you are under stress several muscles in your body tense involuntarily, particularly in your back and your neck. It's very subtle, you don't really realize that your muscles are tense, your body simply gets used to it. Over time all that tightness and pressure causes pain, but because you don't consciously feel your muscles tense it feels like it's coming out of nowhere. It's like having a broken arm, but on the outside the arm is perfectly functional, all you know is that your arm has inexplicable pain from time to time.

Long term stress causes all sorts of fun on your body (and your mind for that matter). I don't recommend it.