vr6 engine bogging down

02 gti vr6.. What causes the engine to hesitate/cough/sputter when I shift into 2nd gear after winding out 1st gear. I don't power shift into 2nd, it's more of a speed shift but I do push my foot (after the shift) to the floor trying not to loose any RPMs...It takes 2 or 3 seconds for it to clear up then 2nd gear kicks in. Back in the day of muscle cars we called it bogging down. It was a fuel and timing issue...Any thoughts?