rough driving

Lets say i'm drivin for 1/2 hour. i go to the gas station turn of the car for 5 min. I go to turn the car on (while the engiene is still warm), and it runs rough, like bad timing, so you drive it for a little bit and it goes back to normal. WTF is goin on, it can't be bad head gaskets, it did it when the engiene was new. Could it be a fuel pressure problem, MAS sensor problem?

thanks for the help