Prior to v3.xxx, I was able to load Nintendont via USB Loader GX to auto-load GC games. With v3.xxx, the line that says the size of the USB drive shows this instead...
Drive Size: nanGB Sector size: -1
It then proceeds to lock up after stating "Loading config... Done!". This is with no other USB device other than the drive with my games connected. If I load Nintendont from the HBC or from USB Loader GX without auto-boot enabled, it works fine. In such a case when loading from USB Loader GX without auto-boot enabled, it does point to the correct device and, within that, the game I chose from USB Loader GX.
Regarding having 2 drives connected (a Wii U drive and a Wii drive), it seems a lot of apps are not checking Port 0 first, but Port 1 (or are exclusive to Port 1, as I can't get USB Loader GX to work on any other port but that). While it's probably not possible to just ignore the Wii U drive, what about having it start with a different port and circulate through the rest if it finds nothing in the current port (like rather than doing 0-1-2-3, allow it to do something like 1-2-3-0 instead)?