This problem was driving me crazy for months! Today I finally solved it by myself, since I couldn't find any answers that worked for me, because of that I'm making this thread to document on how I solved it for future users:
Problem: 500GB HDD (only one partition) FAT32 and 32k cluster size working very well on USB Loader, Nintendont and WiiXplorer. But on Snes9x, VBAGX, Wii64 and ScummVM I either was getting the "usb drive not found" error or just couldn't see the USB drive at all. This problem was making it impossible to load ROMs from the HDD, but I could load ROMs fine from the SD card.
Solution: Check if your drive is using the GPT partition scheme, if it's using that scheme, that's the problem that's preventing the emulators from detecting the drive, use your favorite HDD partitioning software to convert it to the MBR partition scheme, be aware that some HDD Partitioning programs will format your HDD to change the scheme so backup your files so you wont lose them (I'm looking at you nintendont savefiles), if you don't want to format it use the EasyUS Partition Master, it can change the scheme without formating the drive
Problem: 500GB HDD (only one partition) FAT32 and 32k cluster size working very well on USB Loader, Nintendont and WiiXplorer. But on Snes9x, VBAGX, Wii64 and ScummVM I either was getting the "usb drive not found" error or just couldn't see the USB drive at all. This problem was making it impossible to load ROMs from the HDD, but I could load ROMs fine from the SD card.
Solution: Check if your drive is using the GPT partition scheme, if it's using that scheme, that's the problem that's preventing the emulators from detecting the drive, use your favorite HDD partitioning software to convert it to the MBR partition scheme, be aware that some HDD Partitioning programs will format your HDD to change the scheme so backup your files so you wont lose them (I'm looking at you nintendont savefiles), if you don't want to format it use the EasyUS Partition Master, it can change the scheme without formating the drive