Your current problem is likely caused by:
I thought about the jumpers too, but if the computer can see the proper hdd size it should be properly set. but maybe I'm wrong, I'm not very good with jumper setup.
Just few things I'd like to mention, don't take it bad, I just want to inform everyone interesting. we had the "active flag" rumor circulating for 10 years
• The Wii doesn't support a specific USB format, both MBR or GPT are up to the launched program to support it.
GPT is working with few homebrew but not all. Maybe not snes9xGX but he said he formatted to MBR.
System menu supports MBR for the SD card, IOS59 supports WFS HDD (no partition table, like the wiiu), and some usbloaders also supported WBFS with no partition table.
theoretically, homebrew can load up to a 16TB partition.
• Active flag on the partition has no effect on Wii homebrew.
Active is a flag used by computer BIOS to know which partition to boot at computer's power on.
• The Wii "firmware" version has no effect on the HDD detection. the version (3.2E, 4.3E, etc.) is not a firmware but only the version of the system menu application launched at console boot.
the console can launch anything else at boot (priiloader, hbc, etc.) and it will not care what the version of the system menu is. The menu is not in memory at all, and has no effect on retail game compatibility or homebrew.
the only thing responsible for the hardware access and compatibility is the current IOS loaded by the currently running application. You are right he may have an outdated IOS58 (the IOS used by snes9xgx) but I don't know if it would affect its enclosure detection.
That doesn't prevent him to check his current setup and see if it requires an update or not.
Maybe posting a syscheck will tell us if the IOS are old or not, but my Wii is still on 3.2E and I still miss few IOS that I never needed, it was never a problem for hdd compatibility at all.