I'm not sure if it is a glitch but diplomacy will disappear if you refresh. It will reappear in a few weeks. For me it's every 3-4 weeks. When it reappears, don't refresh or it will be gone for a while.
In order to add to auto-route, just make sure they are the same type of cargo ships as are already in the auto-route you wish to add too. The option to merge with auto-route will be in the ships you are trying to add (Scroll down).
 "Heart of Galaxy: Horizons"){kind=icon}
 "Zombie Tower Defence"){kind=icon}
 "Medieval: Age of Honor"){kind=icon}