We've done tests on the server with persistence enabled and we are still experiencing the same problems. After disabling it all the issues seemed to disappear. This is even after last weeks hotfix which was supposed to have fixed the persistence corruption. We've now had GameServers permanently disable the persistence on our server, and all other local server admins/owners have followed our example and did the same thing (otherwise the game is unplayable).
On a further note I would like to add that there seems to be an additional issue with the loot respawn mechanics on persistence enabled servers. Nothing seems to respawn even after all the buildings have been emptied and the items that were in there were used or discarded.