Q: why does my transmission shift hard from 2nd to 3rd

So i literally just had my transmission completely rebuilt 100 miles ago. every shift is perfect except i still get a little bit of a kick on the 2nd to 3rd which was one of my main issues at first anyways.. the shop i took it to is extremely reputable and has been around a while so ofcourse i brought it back and the owner took a test drive with me and said unfortunately thats just how the FNR5 transaxle in this vehicle is... but he said if it doesn't smooth over within 1000 miles to bring it back and they'll fix it again free so I dont think hes trying to weasel out of the warranty.. some other owners i've talked to say the same thing. they got rid of the car because that's just how it shifted.. is this the case? He also made sure to use the motorcraft FNR5 specifically designed fluid for the transaxle as well as setting proper level..

我的汽车有65080英里。
My car has an automatic transmission.