D800E in CMD mode. Built-in flash TTL Comp 0. Group A TTL Comp. 0. Group B --. Channel 1.
Flash sync normal (not slow or rear).
I just tried 6 shots in a dark room with no obstruction between camera and SB-800. 4 were black, 2 lit. The black shots had no light from the builtin flash. On the playback screen the flash fields of the dark pictures are blank as if flash were off.
The lightning bolt flash icon appears in the viewfinder.
AF-S or AF-C don't seem to matter. I use single point autofocus; choice of focus point doesn't seem to matter. (I wouldn't expect either to matter.)