You can see that in one of the images, the rain appears to be falling in my house despite there being blocks above. To test, I went down towards bedrock, and despite there being PLENTY of block above me, it still happened when I was almost at bedrock. I also happened to notice that the rain cannot be seen everywhere like it usually would be, and instead is very patchy.

NOTE: I restarted my game when I first ran into this, but it did not help and this still continued to happen.