@Kaarosu
Your patch is indeed changing the ID of the game, so.. are you sure that you are using NitroExplorer to update edited files?
With NitroExplorer, a lot of issues will be fixed. DSLazy and another programs that use that as base, changes automatically the ID, because the .nds file is rebuilded.
Also, in the file structure, which are the files edited at the moment in v3? All folder 0 files?