The WHATWG doesn't bother with versions, there will be no HTML6, for example. They just continually update the HTML5 spec. It's a living spec.
The W3C kind of tracks the WHATWG progress and tags certain points with version numbers (that's where the "5.1" comes from).
Although they do some development on their own, and sometimes both sides disagree and the specs diverge. At some point WHATWG removed an element that W3C retained or the other way around.
I have no idea if they still diverge. I just discard the W3C when it comes to HTML5 and follow WHATWG.
Well, practically speaking, I follow what the Mozilla Development Network documents. :-)