I remember my own flying fingers, and they only seemed to fly when I was playing the top E and B strings. Try as I might I had the same problem as you, and couldn't seem to control them.
For me however, it was a wrist position issue. I found if I dropped my thumb further down the back of the neck, the amount of lift in my fingers instantly reduced. That, and a lot of metronome work solved the problem.
Good luck with it!
"I like to play that guitar. I have to stare at it while I'm playing it because I'm not very good at playing it."
Noel Gallagher (who took the words right out of my mouth)