Rain only occurs over generated bodies of water

Rain only falls over auto-generated bodies of water (see http://gaming.stackexchange.com/questions/255660/why-is-it-raining-only-over-generated-bodies-of-water for a question I asked on the Stack Exchange network about the issue).

To reproduce, simply stand over a natural body of water (river, stream, lake, sea); it'll rain. Now go onto land; it will not be raining (even if in the same chunk).

YouTube video showing the issue: https://www.youtube.com/watch?v=Kifz8BSZgbc&feature=youtu.be