I trimmed down my mission to make the saving and loading faster and did some testing today. I should have pointed out in the original post that we use R3F Logistics and the Creation Factory to obtain all the equipment etc we need in the mission.

I have found the following:
If you use R3F Logistics to move the objects then the Alive Logistics module doesn't recognise them.
Once you use Alive Logistics to carry and then drop the object the module registers the object and persistence works.

My question is now, can Alive register the object via R3F move and carry instead of needing to use the Alive Logistics? R3F lets us put sandbags on rocks, or double stack sandbag walls etc which is really useful when you are building a FOB while Alive Logistics snaps everything to ground level when you drop it so an object placed on a rock disappears under the rock.