Being able to load your Wii games off the HDD drive works differently. Wii games are loaded natively via USB Loader GX (or which ever USB program you use) where as DIOS MIOS handles the GC loading. Your USB loader simply calls upon DIOS MIOS to do the loading of USB GC games rather than actually doing it on its own, surely the 2 are working with each other (can't say for sure cause I didn't work on the program) but being that DIOS MIOS is its own thing it has different USB HDD compatibility that Wii USB Loaders do.
By the way, Which revision of USB Loader and DIOS MIOS are you using? And how are you launching it (via Forwarder Channel or HBC)?