Invisible SAM/AAA/radar sites have really held up development of my new campaign.
I've got the problem solved now, but it took a lot of trial and error. You should be aware that this isn't just a matter of how many plugins you have. Their type and proximity are also factors. Replacing a large SAM/AAA site with a small one, or moving nearby sites slightly further apart can sometimes fix the problem.
My template includes stuff from F-15 (SA-2, SA-3, SA-6, Big Bird & Flat Face GCI) so I can't really pass it around.