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1) you might want to look at the crank sensor .Ive read on other forums that a bad crank sensor will throw a transmission malfuntion warning.... it could be the issue, ive read on other forums when the dealer was saying new transmission,, and it turned out to be the crank sensor

2) on my car a transmission malfuntion error would pop up and after restarting,, the car codes went away .. then back again..i dealt with that for weeks.. look into a alternator have it checked and your battery.. when ur alternator starts to go bad and stops charging for seconds at a time..and creates low voltage.. and the car gets really screwy... these cars are really power hungry and very sensitive to low voltage. Once i changed the alternator problem was solved... if u start getting more errors like ARS malfuntion,, dynamic drive malfuntion,, ABS malfuntion.. along with transmission malfuntion.. the alternator is the culprit... hope this helps you out and i think one of these two options,,, is probably ur solution to the problem