So, I feel dumb. Seems to be a naming issue.
All games are in sub directories called "Game Name [GAMEID]". But, the files names of the ones that work are simply named GAMEID.wbfs. The ones that don't were named "Game Name [GAMEID].wbfs". I'm assuming [ and ] are illegal character in the name...
I am having this strange issue. I have a 16GB FAT32 flash drive that my games are stored on in wbfs format. Seems to work great for the most part - I can play New Super Mario Bros, Wii Sports, and Super Paper Mario from it.
However, I also have Donkey Kong Country Returns and Monster Hunter...