I just had this happen and replaced the head unit for nothing. Mine started losing the right speakers then lefts then I would hear the tower speakers start doing the same. It did it with the iPod,CD and radio so I thought I had a bad head unit. Replaced it with a CMD8 and had the same problem. Started watching the amps while the problem was happening and noticed they would dim or blink quickly. I switched the battery switch from on to both and the problem went away.
So what I found was that I had switched the battery that I use to power the boat lift to the battery was the sound system was attached to. Apparently the lift was draining the battery and with the sporadic use we give the boat the battery wasn't able to charge up after a day on the lake and the draw from hoisting the boat out of the water. So l took the battery home, charged it up and put the lift plug back on the starting battery. Not a problem since.
Sounds like a low battery could be your problem also. I'd take them out, get a good charge on them and see where you end up from there. Or you could spend a bunch of money like I did and then charge the batteries.