I have had a similar problem, I made 3 flights to depart from Lincoln, the flight I was lead of spawned around the deck and were blocked by other aircraft set to depart on a switch latter in the mission. I could taxi as I was in the first spot near the forward cats, but No. 2 spawned just forward of the island in a slot blocked by other aircraft. I have tried numerous ways to overcome this and the only way was by using LATE ACTIVATION, which sort of ruins the effect of a deck full of aircraft on start.
Would/Could it be possible to select slots for AI as at an airfield, then it would be possible to prevent a latter departing flight from blocking an earlier flight.