Another followup, with I think may be my own personal solution (may not work for you). First, I should mention that I'm using two Commander Pros and two fan RGB controllers. The secondary Commander Pro and one of the RGB controllers is hooked to the primary Commander Pro and then the other RGB controller is connected to the secondary Commander Pro. Yes, I know it isn't officially supported but I did it anyway. Because I'm dumb and didn't feel like dealing with a ton of Y-cables. Anyhoo...
I have a ASUS ROG Crosshair VIII Hero. On the motherboard, there are two USB connectors. One had the case cable for the front panel and the other had the primary Commander Pro. When I turned my computer on today, the secondary Commander Pro and both RGB controllers were not being recognized by the computer. No amount of restarts or even resetting my motherboard worked.
So I believe this told me either it was the motherboard or the main Commander Pro that was causing me my problems (remember - Aura was completely uninstalled and turned off in the BIOS settings). Since I have all the cables nice and tied/wrapped all prettily, I didn't want to try to move the secondary Pro into the primary spot. In absolute blind hope, I traded the two USB cables on the motherboard.
For some reason, it works. I was even able to reinstall Aura and get the rest of the RGBs to work (flow indicator and pretty ROG lights on the motherboard). Honestly, I don't know why it worked but I'm really hoping it's just some sort of BIOS setting that I'm not aware of, simply because the only other option is that my fairly new (barely 4 months) motherboard has gone bad already.
So, yeah, that's where I'm at. The Commander Pro is in the right-hand USB connection now and everything seems to be working as it should.
Take from it what you will.