I don't think that a different wad manager can make it work or not. A wad is a wad, installed with wad manager, MMM, or anything else, it should work the same.
I used Yet Another Wad Mod Manager
my setup :
PAL Wii (3.2E)
Nintendont (latest version : 1.20, renamed boot.dol+meta.xml+icon.png) on both my SD and my HDD (partition 1, FAT32, used also for my GC games) so I can use it alone (from SD) or with a loader (from HDD)
priiloader patches (block online and DVD update, replace start menu with back menu)
official GC pad
Parameters : memory emulation, nothing else
Do you have meta.xml in the same folder ? (apps\Nintendont)