Official comment
@Michael > You didn't call the hot cues for the new track. Either set the preferences to auto-load the hot cues any time you load a track, or manually go into the hot cue page and press and hold the CALL button. The advantage of NOT having hot-cues overwritten is you can load a hot cue BANK which has the ability to have a hot cue from any song in your collection stored and ready to fire.