What is causing a stutter in the new transmission?

What is your question?

I have had a rebuilt transmission put in twice. BOTH times we have a "stutter" (not a slip) from 3rd to 4th gear. Even slipping a little in the 1st to 2nd (that is new to me but figuring it is part of the overall problem with the transmission). I can go around the stutter (some times) if I gun it and avoid the 1700rpms in 3rd gear. HELP We are 10,000 dollars upside down on this car so trade in will realllllly hurt. It obviously isn't the transmission. Have you had the problem and what fixed it? THANKS