I think I can help with this one.
Anything you spawn or place in the map needs to be synced to the Alive Virtual AI module. The reason is actually rather simple. when you sync something, you are telling Alive to manage it, at which point Alive takes over control and then respawns the object.
If you don't do this, when the mission starts, Arma places the object itself and then when you save it, Alive creates a copy in its database which it then spawns on reload in addition to Arma placing the original object. If you check inventory you will notice one vehicle always has the original loadout
This is a big problem if you place a lot of objects though, so sometimes it's easier just to sync the main character to Alive, which you would normally NOT do, then tell Alive to virtualize all non-synced objects instead by editing the module.