Keypad woes...
I had the same issue, but mine is still under warranty. I've owned and played with these for decades, in fact I have a 25 year old with the system, so I know them inside and out. I tried every trick I could think of without success. I even stumbled across the code that worked every time... Unfortunately it was the same button 5 times. The factory code never worked nor did the one I would program thru MFT. The dealer spent about an hour with the car and returned it as now fixed.
Sidebar:
They gave me the code which was the same buttons as the factory code, however the tech just used odd numbers. I indicated O.K. that is the factory code I have. The tech disagreed and indicated he had no idea where I got that from but xxxxx was the code! It was a funny conversation pointing out that code 13579 is EXACTLY the same as code 24680. The tech was miffed even tho I went out of my way not to insult him.
Anyway, I went to the car and after about 5 tries, I got the code to work. They came out and were wondering if there was a problem. I indicated it worked, but I must need to learn how to push these buttons as I am struggling to get it to work. I have been able to get it to work about 1 in 7 - 10 attempts. Further the code I entered thru MFT has only worked once.
I think the keypad itself is defective. I recommend you try the same number 5 times and just go down the line to see if that does it. If it works you will need dealership help to correct that. From there make sure it works each and every time before leaving the dealership. It may save you a return trip!