My roof leaks. I went around and patched it, but it keeps coming back when a different type of storm appears. I could not replicate in a new game but the conversion from 20w16a all blocks that were in place the rain seeps there, and I mean all the way through walls with more than 10 blocks high. I don't know any particular block that causes as I have seen it go through Stone Brick, Black Stone Brick, Red Nether Brick and even the Mushroom light, so I don't think it is block related, but is something in the Rain algorithm. 

The additional screenshots show it is going through my outer wall, and down 6 floors of storage (5 blocks high plus 1 for the floor) all the way to the bottom passing through everything, hoppers included.