Well, first off, I'd reccomend installing the latest cIOS if you haven't already, which can be found here.
Also, I'd read around for dop-ios, which allows you to update your ios's as well as install ios's that you do not have installed and keep the trucha bug intact which allows you to install wads and such.
Now, you're saying you're using DVD's to play the games off of correct? Which loader are you using Neogamma?
For NSMB, read this. There was a new type of anti piracy included in the game and requires a patch in order to be played on modchips and loaders.