on the online game, it seems like there is instability at the beginning of the month. This may be due to a problem with the factory placement function, as it only started happening when new industries were being placed on the map by the game.
At the beginning of the month the routing tables are recalculated. I am not sure the code is not pausing according to calculation power. If something is distributed during recalculations its route will change due to the state of recalculation => desync.
Changes made during an ongoing centralised search have already been taken care of, and thus would not lead to desyncs or crashes.