Carbon M, I think I am seeing some of what you are talking about. Under "normal" conditions from a stop sign, the transmission (It does now after the latest transmission reprogram) starts out in 1st with a light throttle to about 1500 in all gears to 3 rd and can't tell what gear it is in after 3rd but seems OK to about 40+ mph.

But if you take off from a stop about half throttle, 1st shifts out about 3000, but 2nd shifts out about 5000+, 3rd about 3000 - 3500 then all other gears 3000 to 2500.
Under a full throttle start about the same.

Seems like only second gear for some reason wants to go to 5000 or more. Letting off the throttle a little in second thinking that it would shift to third does not seem to help much, so you have to let way off the throttle, then it shifts to third, under a half or full throttle start or let it shift itself out of 2nd at 4500-5000.

Why does 2nd need to shift out at 4500-5000 on a heavy throttle start when the other gears sfift out by 2500-3000?
Ford only knows. (or don't know)

I really don't notice this as watching the road and with the radio on, so I was not watching the tach much until now.
May be this is a gas saving feature to keep a lighter right foot. So I just get in the habit of starting out through 1st and 2nd with a lighter throttle and then give it the gas in third if you need to get going other wise it is going to go to about 5000 in second.

I have learned to live with it, and have not taken it back to the dealer yet as it is working so much better now than it was before the last reprogram.
Before the last transmission reprogram it kept trying to take off from a stop in second gear, then down shift to low, causing a jump from a stop light.

Sometimes they can fix one problem and then cause two new ones, so for now I am holding off going to the dealer unless it gets worse and it does still get me from point A to point B. (only 600 miles on it)
It gets confused sometimes on a forced down shift, but it is not really a problem as you just let it do it's thing until it decides what gear it wants, then gets going.

I don't notice a problem coming to a stop. But I will say that after the last transmission reprogram the idle speed seems a little higher, but has not caused a problem yet.

I really miss my old 5.8 94 Bronco, shifted flawless for 100,000+ miles.