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Yeah it sounds like you don't have something connecting properly. If they didn't spawn at all then you may not have the objectives connected properly but without seeing what you have it is difficult to diagnose.
When setting up TAOR's I have found that if you have them touching it seems to over ride whatever blacklist you created. Also you need to take a look at the settings for how you have your units spawning. Lastly the map itself may not be indexed correctly so you will want to setup custom objectives and smaller TAOR's related to just those custom objectives.
Once you sync aircraft to the MACC they get whatever orders the MACC has for sending aircraft around. That would be depending on what mission types you gave the MACC to load in for the BLUFOR/OPFOR OPCOM to populate. So they can be doing CAS, CAP, SEAD, Recce, etc... Just because the ATC is recognized as an HQ does not mean that the airfield was indexed with the correct settings to recognize the hangars as places to place aircraft.
In that case you will need to go in and place invisible markers for the aircraft to be placed. OR place them into the mission before you upload it. If you don't want aircraft rolling away you can pull the fuel out of them or placed them into the mission without crews in them and they will not fly away.
Did you setup a second OPCOM that would be controlling the second insurgent force and link them to the BLUFOR objectives?
@marceldev89 we have noticed some issues recently with our missions not saving persistence and getting extremely bogged down as well. That is why I was interested in what @Yeti may have found. I will point our mission guys to what @JD_Wang mentioned and we will go over the CQB settings we have as they might be the ultimate culprit.
@JD_Wang @RedeyeStorm in our current mission we are using 3.0 and have not had a problem with any thing like that. In fact we had a QRF early on in the mission from our BLUFOR AI support element that did an air assault into a town to support our players while they were being assaulted by a massive insurgent force on Reshmaan. Other than the BLUFOR AI spawning in and using the wrong helos for the mission they did everything else correctly. They landed both Ghosthawks in open areas outside the town and then waited until the troops were all out before lifting off. Then they flew limited gun support with their door gunners as they were on their exfil route from the LZ.
Also you have to link the objectives you want one side to attack to the other commander.
Take a look at the wiki and click on the quickstart link and it should be one of the first things it shows in there when you go to it. You can use this picture here to show how it will appear with the lines on the screen.
Yeah I personally can't get beyond the initializing waterfall screen.