the loader is supposed to load the themes you currently have.
The ressources are loaded automatically from the NAND.
Maybe your theme files are not standard format or size, or wrong color palette etc.
Or maybe the USBGX resource loader is not working with all possible/known format.
I never replaced themes on my console, so I can't help you there. I'm not the one who coded the ressource manager/System menu emulator.
Maybe you could ask diddy if he knows anything about theme format which works or not in this loader.