I'm having the same problem. I have d2x-v9-beta installed in cIOS 248 (with it set to 248 in the options of USB Loader GX), and I have the latest USB Loader GX version r1203. Any Virtual Console or other channel I try to run that's in the EmuNAND, it just resets the Wii. I already did a full dump of my NAND into emunand, and the paths are properly set up in the options. Any suggestions?
EDIT: OK, I might be on the right track. Would it screw things up to dump your NAND, go into System Menu, delete the old NAND, copy more things from the Wii's official SD into NAND, and then dump the NAND again? Because that's what I did. It seems that any of the apps I got from the original dump don't work, but the ones from the second dump seem to work...Is there any way to fix that without deleting everything and re-downloading from the Wii shop (or any other WAD source)? I already deleted the first batch from the NAND, because there's not enough space in there for all my games.
EDIT2: No never mind, as soon as I delete the copies of them in my normal NAND, the emunand ones stop working. Any tips?