When first mission gets created, I noticed that some planes seem to air start and fly off to an offmap airbase. In an attempt to fix it, I changed the names of the carriers and lo and behold it works.
The problem crops up when I get onto the second mission, ALL the planes exhibit the behaviour where they get an armed recon mission then land in an offmap base. I basically changed the "Master" version of coral seas.
Edit:
I was using dcgen 348 beta 7
Installed on IL2 1946 4.12.2 unmodded
Playing coop multiplayer campaign.