Hammer does this sometimes, usually when there's an error that vbsp hangs on early, i.e. before it even creates the bsp. There are a number of things that have caused this for me in the past, the ones that spring to mind are having a displacement tied to an entity or having a displacement with no rendered faces. I think it can also be caused by non-areaportal brushes being tied to an areaportal entity or a brush intersecting with a sky_camera entity. I can guarantee any of these are the cause but I think they are potential candidates.
On the other hand I have had this happen at random, seemingly because hammer had a brainfart, and like your issue it somehow magically resolved itself. If it happens again try checking the errors I mentioned, if not then count yourself lucky!