Reflew the mission. Waited until the pilot (me) sighted the airfield and ordered the attack (there is a voiceover where he orders the attack automatically). I then Used F10 menu to order the attack. This time the F10 menu had to option to attack primary (as opposed to attack primary and rejoin). Ordered Flight, second element and wingman to attack. They all did, and the mission worked fine. Issue solved. Maybe I ordered the attack too soon the first time around.
Pappy_Gunn's post in A couple of bugs (?) was marked as the answer