Quote Originally Posted by Bin_jammin
It's probably your EGR. Or a vacuum leak.

Seriously though, what did your tune include? New wires? Resistance check on them? Check the plugs? Do you mean it starts to stutter while you're traveling down the road?

New fuel filter done with the tune? Post more info, please, it will help with diagnosis.
+1 need more info but a bad fuel filter will cause some slight hesitation