I haven't played Minecraft for a while: is this a recent change that I missed? I first noticed this on a server so I tried single-player, but however the issue persists.
I've tracked it down to generated bodies of water (e.g, not water that the player has put down or any part of the world that is modified where water flows), that is:
If I dig a large hole and fill it with water from a nearby natural water source (where the rain is falling), rain will not fall over the body of water I created.
Thinking that this was an issue with the GPU, I upgraded the GPU (small upgrade, but a huge difference and I needed the upgrade anyhow) but the problem persists. I've also tried reinstalling the game (I have not tried an earlier version (snapshot) of the game however, and I'll do that shortly) and that didn't work either.
I have this issue in the Savanna and Desert biomes, and I haven't tried another biome type.
What's going on here?