Hey neat intro approach on that mission with the ride up and eject on mission start. :) In fact, I liked it so much and was bored, I made some edits for you (explained below):
Ok so, the main problem was, you didn't have the Player Options module placed. In that module, you can set player position to be persistent (make sure it says yes), and you also have to have "save to database" I believe it's called, set to yes in that module also. I think what was going on here was, without this module placed in your mission, your player position wasn't saving, and that made it seem like nothing was loading. If that's not the case, let me know. Anyway, I added this module to your mission above so check it out!
Other things I edited:
I'm not an Air Commander expert or anything, but pretty sure you need to define that airspace. Anyway, I added that (blue "airspace" module, also written as an override in the Air Commander module).
I added a small marker around your starting base to try and keep any friendly vehicle spawns from spawning directly in it. I named the "noexplode" and placed it directly above your little base, and added the marker name to the BLU Civ Obj Placement module blacklist.
You had some vehicles exploding on mission start at the main base also, so I moved them. I also double clicked on both of your camo cargo net thingies and disabled their ability to take damage so they don't flatten like a pancake in the event you or you AI ever hit them or spawn ON THEM.
I moved forward your spawn position because 100% of the time, the AI group following you in the vehicle to the base thingy on mission start, would crash in that town because Arma AI blows. Now they don't have to worry about hitting anything (though they still drive like madmen lol).
I also removed your Unsung dependency. Now this mission ONLY REQUIRES ALiVE and CBA and nothing else. This leads me to believe maybe you made this mission on an Unsung map and didn't think of telling me (FOR SHAME!!! :) ) so now to punish you your mission is set on Altis. ;)
It is saving for me, or at least it seems with a quick test. FYI if it doesn't for you, grab the new PBO with a persistence fix in this thread (it shouldn't apply to you here, but I was using it when testing your mission): http://alivemod.com/forum/4034-mission-not-saving