I have been ripping the audio tracks from several of my DVDs. Everything has been fine except for one, The Emporer's New Groove.

I use DVD Decrypter and then DVD2AVI which provides the audio in a WAV file, but in this case the audio output is a few AC3 files.

Am I doing something wrong or is this disc encoded differently?

Most DVD's use AC3 audio. Just run the AC3 through HeadAC3e or BeSweet to do a dolby downmix to wav, mp3, mp2, ogg, etc.