Sorry to hear about the issue...I have been addicted to my car audio since birth nothing is more depressing to me than a broken stereo
I would suggest it is a connection issue/cable issue from the audio source to the speakers. however, Is there a static like sound as they cut out or just a sudden loss of sound followed by sound playing from the speakers? (scratchy sound while cutting in and out or a clean loss like hitting a mute button on the TV)
Should help determine if this is a connectivity issue, amplifier issue or an output channel on the head unit dieing.
If your under warranty-save yourself the worry and head to the dealer
Good luck