My 06 does this even with a 1 piece drive shaft. Always when turning and shifting, never when going straight. I figured it must have to do with the rear end, because nothing changes when turning, but the angle of the axle.

 

Entirely diffrent thing. I had an 08 that did not do this 1-2 clunk. Its like a VERY had shift in an automatic. It only happens when shifting fast. If you let the clutch out slow its ok.