Let me start by saying that by no means am I an expert in the field of electronics or stereos for that matter, but I hope this helps.
Since the design and quality of these Boom II systems are less than stellar and there is no protective circuitry to assist us, we can be our own worst enemies when it comes to blowing these things up. I believe what is happening for some, other than Harleys vendors building a sub par product is something called "clipping" that can be avoided with a few simple tweaks. It is possible and very probable that our systems settings are set by some of us such that they are making our stereos work outside of what I'll call their comfort zones. When you guys get a chance, take a minute and go out to your bikes, in you garage, and check your audio settings. Your bass and treble settings should NOT be at 11! The center of each level indicates "flat" or no + or - gain. That is your default setting. Give your various sources a listen at that setting for both bass and treble up to a pretty good, say 1/2 to 3/4 volume. Then you can adjust each of those settings a little and to your liking. Try not to go more than a couple of clicks right of center for your bass and maybe as many as 4 for the treble. Also keep your AVC (automatic volume control) set no higher than 2 or 3. Then check max volume on each of your sources (AM, FM, CD, USB, Bluetooth, etc.) and make a mental note of how high you can go before you here distortion. That point of distortion is where you'll start breaking things.
Again with no protective circuitry you can accidentally over drive these systems very easily and break things. Ever turn your car stereo up so loud that it gets to a certain volume and won't get any louder but the knob keeps turning? That's protective circuitry! With our ears either being exposed to the wind at 80 mph or covered with a 3/4 or full faced helmet, it's really hard to tell if our systems are being overdriven to the point of distortion.
I'm not saying that Harley in this case is not to blame but.... just because you can't hear that favorite song of yours distort from overdriving your system doesn't mean that it's not.
Hope this helps.
As a side note if anyone notices that the woofer portion of one of your Boom II saddlebag speakers has blown, you can open up your saddlebag lid and unplug just the woofer part of that speaker until you can replace it. You can then enjoy your stereo without that annoying sound of a broken speaker.