The same thing was happening to me in the winter for about 3 months, a few mornings every week (on weekdays).
I have a close friend who is an ER nurse, and she told me that it was caused by a combination of things....
Stress- The worst culprit- it causes xtra stomache acid, and if you go to bed stressed with little in your somache, it will sit there irritating you- if you could sleep for longer, your body would work on neutralizing the acid- I think this was my problem because i was going to school in the winter and sleeping 4-5 hours a night.
Also, if you eat a big meal before bed, your digestive system works very slowly at night, and when you wake up after only a few hours of sleep, you haven't had enough time to digest everything from the night before...
Lactose intolerance- what could be left churning in your stomache is the stuff you do not have the enzymes to digest, like milk products, etc. and that's all that's in your stomache- It doesn't feel good, and just wants to exit your body fast-
I found that a piece of toast and tea helped alot.
Smoking- usually smokers produce xrta stomache acid anyway, so a smoke first thing in the morning can push your already acid stomache over the edge....
DT's- like someone mentioned before, your body can also be suffering from cravings for nicotine & alcohol if you were partying the night before- on the weekend, you would probably sleep through this hangover, but you are more sensitive to it after only a few hours of sleep.
.......anyhow, i found that the best cure was to drink a glass of water before bed, wait a while for a ciggarette after waking up, or
Pepcid AC acid controller pills are great- a little pill lasts for 12 hours- these always work for me!
i think the main cause is stomache acid that you could normally deal with if you had more regular rhythms