"Do you have any way of narrowing down whether it's the amp that stops making noise or the player? Some amps have an indicator LED labeled "protect" or something like that... "
Mine is definitely Rio-related, since the amp I'm using is from my head-unit's built in amp. Altho my Rio keeps working, the songs don't keep playing like Func. It totally pauses. The time doesn't count down or anything, altho I have seen it mute like Func's problem once. Hijack's reboot function took care of that without having to remove the Rio, turn off the car, re-insert the Rio and turn the car back on. ;p
Sadly, re-loading the Rio's operating system didn't help either. I may be going to the extreme and installing the fan like Beak showed earlier. I've noticed that in the ventholes on the Rio's topside, all I can see is the hd cable... which I imagine is making for a nice air-barrier. If moving that to the side doesn't work, it's fan-installation time.