If an ad break happens during a pause (when a pause trigger tells the system to pause recording), the system ignores the ad cues for the purposes of recording the content.
If the ad break happens during normal recording (after resume/start has been initiated) then the system flags those ad breaks as segments.
If ad breaks happen while recording is paused, the system ignores them and the media isn't segmented.
Be sure to use pause/resume only to omit music or content you do not want recorded (terrestrial PSAs, liners/beds, news segments etc.) but leave recording on during ad breaks in so the system can segment the media properly.