I've been having a similar problem with my '03 4.4i recently (the past ~3 months). When coming to a rolling stop, sometimes there is a jolt when going from 2nd to 1st gear. It also occurred sometimes when I'm coming to a slow rolling stop and then accelerate (e.g. right turn at a light). Pretty embarrassing when having passengers in the car.

I just took my car in to an indy mechanic, and he told me that it's because of the transmission adaptation programming/learning. I guess I've been driving it differently than my wife since I took the car from her back in Nov. Anyhow, he told me that the transmission adaptation needed to be cleared out. While he had it, I asked him to make sure to update my transmission software to the latest version as well. Just picked up the car 2 hours ago and on the drive home (and around doing some errands), it seems to be resolved...hopefully permanently. Actually feels like it's going up/down the gears much smoother now.

Service invoice shows: Reprogram DME, reset trans program learning, update transmission software to latest.