This is kind of a follow up to Windows 98 SE: IDE Compatibility Mode issues

I am experiencing the same or very similar issues.
The author fixed this by setting channels to either none or both. I just didn't know which ones to set on my machine.

Here's a screenshot of the device manager

I seem to have three hard disk controllers. The 4 port SATA controller is not in use for Win98, the 2 port SATA controller is actually only 1 port. I connected the SSD there. It's a Marvell 88SE61111 chip that also serves the IDE connections and maps everything on that SATA port as IDE. The board is the MSI P965 Neo2 and I've successfully installed the ICH8 chipset drivers for Win98.

I'd like to access both my CD drives on IDE so I don't have to attach a USB CD drive (which just works, but, you know...!)
Atm these issues block Win98 from detecting the drives. Also, as a result, my follow systems run in compatibility mode.

Let me know if you need more screenshots or information.

Thank you.