Every single game I have played in 2B has had the structures all invisible.  There are times, briefly, when they are visible - queued & ones under construction show, and occasionally when the build menu is open, all will show.  Otherwise, cloth map or 3d, only the 'city square' is visible.

Happens to me constantly, and in the last build as well.  And yeah zooming out like Daleran said can fix it.  I also have units disappear.  I'll fight some darklings for a quest, and my characters will be swinging at empty air.  Not all the time but sometimes.  I've had heroes disappear as well.