Low blood pressure, low blood sugar, maybe dehydration? When you miss out on sleep, are you in bed trying to sleep and unable? I know for me, low blood sugar will give me headaches, and if I'm awake longer with less sleep my body has expended more energy than normal and needs that extra fuel to function properly. I always wake up starving if I was up late without eating later. When you sleep, your body, obviously uses less stored nutrients to operate. If you're not changing your routine with eating and drinking and you miss out on sleep, you may need water/food. Or it could be stress from lack of sleep tensing you up or you're sleeping at a weird angle because your schedule is off and your body didn't use it's muscle memory and get you into a better position.

Basically, you're going to want to pay attention to the things you're doing (or not doing) besides losing sleep. Eating/drinking, physical exertion, how does the rest of your body feel when you wake up?