I had this happen to me quite a lot in the past but i never knew how i did it.
If you click a brush (select tool) in the 3-D view, then quicky move the mouse (while holding down) to a 2-D window, Hammer cycles through brushes...
Like, every half second the selection changes, i was watching different brushes turn red for about 5 minutes lol.
Maybe it will work. Its hammer 3.4 btw... try it out.