The rain start/stop and thunder start/stop packets are sent to all players in any dimension. 

This affects the client's display of rain particles due to the current dimension not necessarily raining.

changing dimensions updates this info on the clientside. attempting to clear weather has no effect (due to another bug and the fact that the current dimension may not be registered as raining on the server).

This primary affects custom dimensions at the moment but the issue also affects the end and the nether (though those dimensions cannot rain so the visual indicator of the bug is not present).

Code Analysis by linguardium here