Could be alot of things. What do you have? Any Mods?
My truck runs rough for a minute or two, but only if I'm running a tune. There are just to many reasons to post all of them.
When was the oil changed last? Bad oil can do all kinds of things.
Are you running any fuel additives?
Are there any codes? Not all codes set off the light, have it scanned.
How bout fuel filter?
Or bad fuel, But that would probably effect all speeds.
There's alot of stuff to make these things run right. We need a little more information and maybe we can narrow it down for you.