Then it’s time to check all wiring harness connections, ground wires. Any loose pins or corrosion in the connectors?

 

I have the same problem. If I hit the passenger side of the radio sometimes that will knock it on but there has to be a loose wire somewhere. If its a common problem it will probably be in the same place.

 

Update : I rechecked the connectors and the wires, there is a loose orange wire, don't know where that came from but there used to be a bunch of wires coming out of the connector that didn't go anywhere or were initially taped so I assume they're not used. This orange one (just orange nothing else) was loose. I tucked it away.
So what I discovered, was that when I only connected only one of the connectors (the one that brings in power +12v), the sub in the boot worked perfectly, but all the other speakers were out. When I connected the other remaining one (that's two connectors in) , the sub started crackling, the front door and tweeters worked perfectly (as usual) and the rear door speakers were out.

 

Have you checked the front to back fader control... It's in your radio settings.

 

Yes, putting it on back brings out nothing, while putting it on front makes the fronts work.
The left to right, however is weird. When on left, both working sides (front door and tweeters) of the speakers work. When in right, it goes off. But the right comes on when set to only left and mid.
I'm going to try a continuity test in the connectors when plugged in to check for shorts.

 

Haven't checked the short is yet (will, soon).
I've been looking on Google at pictures of radios of the hhr, I just realised that none of them look like mine.
The ones I saw, the fan was on the top, upper left (or lower right) on the top panel.
Mines on the right panel (looking from front), lower center.
Has mine been changed? I'm beginning to think they swapped it.

 

They all look like this. Some have a audi plug instead of the USB port.

 

Radios aren't related to the fan.

 

Some radios have a cooling fan, depends on the vendor GM used a few different ones.

 

If you have a factory subwoofer you have the Pioneer Premium speakers. That system has an amplifier behind the subwoofer that powers all the speakers. The means it needs an audio out signal for each speaker. I’m going to guess that each factory radio that was compatible with both the base and the Premium speakers had both a speaker connector for connection direct to the base speakers and a signal out connector for the Premium amp, and that you only connect one of them.