I have the same issue. I brought my bike in for it's 5K and rolled it out with my speakers not working. It was fine when I brought it in. If I flip any switch (Speaker, Cruise, Aux), it comes back for a second or 2. Sometimes one speaker cuts out and sometimes all my speakers cut out. One thing for certain is that its worse when the volume is turned up. I have the bike back at H-D now as it is a warranty issue. Since it broke on their watch, they are attempting to give me speedy service.
My guess (and it's only a guess) is that either a wire got shorted, a ground dropped, something got wet that shouldn't have, or the radio died. I've read many threads with possibilities on what happened. Most often, this is happening on batwings as the fairing mounts used to allow extra vibration. I can't wait to see what happened with mine.
I'm happy it's under warranty now, but I hope that this doesn't repeat after my warranty runs out...
2012 FLTRU - Road Glide Ultra - Big Blue Pearl