I think I have the same problem but with specific characters. Do you have an EU copy of the game? If yes, are the problematic dittos Sonic, Lucario, and Jigglypuff? Because if so, I noticed that the MTB fix doesn't fix voices in the regional "data" folders (it only does so in the main data folder, the one with the most voices). I ran into that issue with Sonic but I'm assuming Lucario and Jigglypuff are the same because their voice files also are in the regional folders (or at least the french one).
First of all, I believe that you should give us more input on the problem itself. Which voices remain silent, because there are certain characters that can't have slot specific voices. (Bayonetta, Cloud, Wii fit Trainer, Robin, etc. ). Or did the mod have an arleady hex-edited nus3bank file for the voice?