Just started with ALiVE yesterday, fantastic mod, this is the only way i've played since the OFP days, but was previously using basic spawn scripts... this is SO much better..!
But i'm having the same problem mentioned above..
I began with the tutorial mission, and set up a base to defend at Camp Maxwell on Stratis. On mission start, a helicopter spawns onto rocks on the SE side of the base, exploding. Sometimes two at a time. Other times, just a paratrooper spawns, harmlessly.
Unable to use the mission three out of five times, i tried moving the base to the main airport instead, but now the choppers spawn inches from the control tower and each mission again starts with a bang..
Only other mods running are CBA and Mao's sway fix.