When watching a recording and you hit the back button. Then clicking on watch button and then going back to full screen for the show you are watching. When the menu comes back up to show you where you are in the movie/show, it brings up the menu that doesn't have the commercial skip indicators. It looks like when the commercial skip hasn't been detected yet. However the commercial skip does still happen. This happens on the latest release of Apple TV and also in the latest beta version.
The only way to get it back is to close the movie/show screen then click on watch and everything is back to normal.
I hope I made sense with not knowing the correct terms.