I had an 06 Explorer 4X4 V8 and experienced the same issue if I didn't come to a dead stop before re- accelerating from a stop or yield sign. It could also be dangerous if making a quick left turn in front of traffic from a crawl. I had the computer re-flashed with no results. I believe that this is actually the way the transmission is designed to work. It would be very noticable and bothersome to those who drive through many yield or stop signs every day. It could also go un-noticed to those who don't. I consider this transmission program very abnormal compared to pretty much every other transmission I have operated. What I consider a "normal" transmission, would downshift from 2-1 while slowing to a stop, not after re-accelerating. I definitely disagree with the logic of this transmission program, and appreciate the quick power and response that I get from driving a vehicle with a "normal" transmission. I do however appreciate the added acceleration of a low first gear, and the smooth shifting that this transmission provides during other shifts.
Despite my dislike of this transmission program, I did however purchase an 08 Sport-Trac 4X4 V8 with the same transmission. The problem is somewhat less significant and bothersome because the transmission seems to do the 2-1 shift slightly quicker and smoother while accelerating, however, the transmission still uses the same unusual logic of late downshifting, instead of downshifting ahead of time while slowing down to a stop.
Overall i love this vehicle and would definitely purchase another one, but I have concerns about ford using this transmission in other vehicles like the 09 F-150, because other manufactures like GM don't have this problem.