Did you get a check engine light? Have you checked for any codes?
Sounds like an random misfire or a misfire of a specific plug, that went away.
I have had this happen 3 times with my stock tune with a newer strategy code from Ford. The first was after a long period of driving short distances without flooring it. The other two times occurred when I was going down long steep grades of a mile or longer, where the tranny was braking the car, and little fuel was going to the cylinders. After the check engine light started flashing my Flex ran very poorly for maybe 10-20 seconds and then was back to normal.
Since in my instance I got both the random misfire code, as well as a specific plug code, but not the same plug on any of the 3 times.
While I don't have a definite diagnosis, my gut tells me that either my injectors needed cleaning, or there is a carbon buildup on my intake valves that is disrupting air flow, like what has happened to DI Audi's and VW's.
If it happens again you need to take it to a dealer.
