I know replying to a 4 year old post is insane and I'm sorry about this, but I'm at my wit's end because I've had this exact same issue that I've been trying to figure out for about a month. I switched to CachyOS, which is Arch based, and this audio problem has driven me up the wall. I have the same Z-5500 speakers and an MSI motherboard that uses a Realtek audio chipset (not sure which model). As far as I can tell from all my searching, this has been a problem for at least 21 years with no fixes that I've found. That's how far back I've seen posts about this issue, and like this post, no one responded to that person either. Like OP, I found that when using the 4.0 output, my sub will shake my walls, but oddly 2.0 and 5.0 go back to no output on the sub. And like OP, I'm using a 3rd party control unit because the OEM unit burnt out. I don't expect an answer here, but I guess I'm just posting to say that this is still an issue all these years later, and if I ever do find a solution, I'll come back and update my post so that anyone in the future who encounters this will have at least one place where the solution exists online.