A mining depot on a many hour MP game had a recipe set for mining an ore and drones in it. The ore had become all mined up while player1 was on the server and the no ore within range alert was going off. When player2 joined the server they got a desync (linked below). Player 1 removed the recipe on the mining depot and then player2 could rejoin.
hmm some time later player3 joined and had the same issue, but we had no alerts up at the time. The deync reports do look like its the mining drones that have the game state variation though :s