Alright, after extensive testing and poking every variable (including which device my EmuNand is stored on and going to default settings), I have determined that USB Loader GX (r1208) may display EmuNand titles just fine, but it will then attempt to load the title off of the Wii Nand anyway. Thus, I can install any title on the Wii Nand and even a 'ghost' title of the same name on the EmuNand can play it (confirmed--with regular Nand title display turned off in the loader settings). Delete the Wii game (regardless of whether I save the title via having a savegame), and even a correctly installed EmuNand title of the same name won't run.
So either I am doing something horribly wrong, or there is something horribly wrong with this version of USB Loader GX. Man, I really don't wanna go back to a version of USB Loader GX/DIOS MIOS that can't run Twin Snakes...
EDIT: While the nature of this problem is now officially over my head, I can still test whether it's the unofficial release of USB Loader GX that's causing my problem. I will try 3.0 and other intermediate revisions I can find, as well as making a "clean plus one" Nand and EmuNand to test the loading source again in case the newer-revision loader's Nand dumping is somehow to blame. I'm a scientist at heart but I know jack about the Wii file systems...
LAST EDIT: I made a "clean plus one" emulated NAND using USB Loader 3.0, played the game successfully, went to delete it from the regular Wii NAND via System Menu, and broke the EmuNAND version--just like every other time. There doesn't seem to be anything unusual in my titles when I look at them using ShowMiiNand and AnyTitleDeleter. I guess the next thing would be to start deleting those hidden channels and see if anything changes (shouldn't hurt anything on an EmuNAND, anyway). Otherwise...I AM 100% STUCK. How do I load games off of EmuNAND instead of just seeing what amounts to regular NAND forwarders???
Note: I have been using genuine and injected NES and SNES games to test correct NAND loading, if that makes any difference. Also, everything is set up on IOS 249, which I believe is using the latest version of d2x.
I LIED, THIS IS THE LAST EDIT: Oh, I decided right before hitting the hay to double-check that I had the latest version of d2x installed. I didn't! Now, when I run an EmuNand game, the disc light blinks twice then happily launches the game exactly as intended!! I think all the VCs work now--only need to test the WiiWare! Thanks all!!