Back in 2.x the in-game time of day was synced between singleplayer, multiplayer, and the main menu. When pausing and the /time and /cycle commands were added this was never properly sorted out. It is on my to-do list nowadays to go back and fix. A lot of code is affected, for example the crops/plants store a real-world time rather than in-game time, so I am not sure when I will fully take care of it.