to reproduce the problem I do not know what to tell you other than that. I Demare Arma 3 if I choose an assignment on all fontionne Stratis (I keep my 40fps) and leads the assignment until the end.
But if I choose a mission Altis departing I have 40 FPS and 2 to 5 minutes after the startup of the mission I find myself 5 or 6 FPS.
the fact I play solo (too bad for playing multiplayers)