Ah, that clears things up a bit. That is a sort of idiomatic construction. Notice that two actions which alternate back-n-forth are being described?
Try to consider it as:
今日は一日中、雨が [降っては止み、降っては止み] (を) している。
You would never see 雨がやんでいる rendered as 雨が止みしている (At least I would be extraordinarily surprised if you did).