One possible cause is a faulty, (dry solder), connection that is affected by heat build up....So as the unit is switched off the joint cools allowing partial connection, as the joint heats back up, (due to high resistance within the joint), it again fails due to heat....
The location of this fault could be almost anywhere from the stock audio loom through to a speakers coil, you could run the unit till it happens again & check if it affects any particular speaker worse by adjusting the fader & balance, if it does simply disconnect it & try again....