Just replaced the transmission and the car still doesn't want to drive sometimes

did you replace the trans yourself ? If a shop did it then they should look at it for free to prove that their trans is not the fault, and at least advise you of what needs to be done if not fix it. to answer your question, if the programming was the problem then I would expect the symptoms to be consistent but you stated sometimes. Need more information on the exact symptoms and when they occur.