I have seen this for previous versions but this is mostly just a post to update previous bug reports as this is currently still occuring in the latest pre-release.  The screenshot is inside my storage room (I have noticed it happen in other places, however this is the most persistant place).  The room is under a hollow mountain and rain seems to only persist under upside down stairs in this room, however also occurs under a dirt and stone roof (part of a custom hill, not sure if this occurs through generated caves and terrain)