Double check your BIOS settings to make sure AHCI is disable for the SATA ports. [Check the user manual for this].
Maybe try to switch the Pioneer and Samsung alternatively between the black and red SATA ports and see if you can find a winning combination.
In Device Manager, there should be an entry for the main controller for the 4 red ports, and an entry for the secondary controller for the 2 black ports. See if the controller for the two black ports [should be easy to identify by the device name] can use standard Windows drivers.
I’m not sure about Magic ISO. I don’t know how involved it can get in the process of detecting drives. If you don’t mind, uninstall it just in case.
Make sure you try the wnaspi32 check I suggested above, since you said that burning was not affected, and that it was only the two standalone scanning applications.