I dunno, I think it's a true fix though, because before running the tool, it threw up the same ARM11 error you mentioned on my N2DS with CFW.Try to redownload the update data, then - maybe it just got corrupted on the SD card, or something.
Will mark this as partial fix, in any case.
Might also be a good idea to use GodMode9 to dump your cartridge to a .cia, extract the ROMFS and compare it with a working one to see exactly what's corrupted.