I've always been using WBFS for USBLoader GX, but since I figured FAT32 or NTFS would be easier to use, since I can copy and structure the files directly without the assistance of Wii Backup Manager or other application (and it's faster, too! 27MB/sec on FAT32/NTFS versus 12MB/sec on WBFS transfers), I reformatted my hard drive and started again.
However, whatever game I load, all in WBFS file format, it just goes to a black screen and never gets to the Wii Remote disclaimer. I'm using the latest version of USBLoader GX, too.
EDIT: I tried to run a SysCheck, but it froze with the progress bar more than halfway across the screen.
Wii (Fall 2007) DMS chipset.