Thanks for all the responses! I went out tonight again and had my trainer watch. Her first thought was that he was trying to scratch or itch, and that her horse and her daughter's horse were both doing similar things/having lots of issues because of the flies (they're awful this year! :( )
It actually makes a lot of sense, I haven't been riding regularly and now that I am it's getting hot and the flies are terrible, and this thing has only started recently. And Nav is sometimes afraid of the fly spray and so I don't spray as much as I probably should on him.
I sprayed him well before riding tonight, especially his chest and front legs, and not once did he do the bob! So for now I'm going to assume that it was simply that he was itchy from flies or sweat or dirt.
I will keep an eye on it all of course, and see if he starts it again. :)