Yeah. Its wierd. Its enough to just have 1 patrol command in the order que.
In my testing I tried having move commands before and after the patrol command but as soon as i added the patrol command gunships would start piling up outside the factory. When I removed the patrol command the gunships moved to the move commands.
I tried disabling luaui with /luaui disable. Then the gunships would go out on patrol from the factory. So... Widget?