OK for edge and cyclo users, whats happening is the v2 patch is modifying the arm7 and the arm9 when all you need is the arm9. If you patch the rom with the v2 patch then unpack that rom you will get the correct fixed arm9 file. You can then unpack the untouched rom and replace the arm9 file with the one you got from the v2 patched rom.

You can also patch the rom with v2 then unpack it and replace the arm7 with the one from the original rom. Either method should work.