It will be caused by the JB! my brother is sat next to me with his JB iPhone and the transitions are choppy and stall on his iPhone 
We are comparing the two iPhone's together opening and closing the same app's and there is a clear difference in the UI transition performance!
On my 3G they open and close very smooth and if i am honest with you the last update improved them even more
i can open and close an app repeatedly without problems 
That's like have a Porsche and putting a Skoda engine in it and expecting the same performance "sorry"
We are comparing the two iPhone's together opening and closing the same app's and there is a clear difference in the UI transition performance!
On my 3G they open and close very smooth and if i am honest with you the last update improved them even more
That's like have a Porsche and putting a Skoda engine in it and expecting the same performance "sorry"