Doubtful. Sounds more like irreconcilable differences over larger policy/strategy issues.
If I had to guess, it's resistance to some sort of proposed change in mission capabilities and/or force structure.
One possibility: the USAF has been dragged over the coals for its poor performance in managing and fielding high-dollar space programs. Could be that Gates is looking at giving some of those programs away to some other organization....
Safe to say.