If the desync happens when you open the logistics window, then it seems like some mod that modifies the logistics window is probably the cause of the problem. Are you using any mods that do that?
This mod doesn't touch the gui at all, or do much of anything in control.lua except set up the proxy containers. Unfortunately, I don't think I can help any more without a way to reproduce the bug, or at least proof this mod is actually the one responsible.