What is the program version you're using? Starting in Movie Edit Pro 12, the program doesn't really use external audio codecs for AC3 audio any longer. You would have to activate the built-in Dolby Digital Stereo decoder to get AC3 sound from e.g. MPEG-2 or AVCHD files.
Also, what is the source material you're using (file type, codecs)? Does it even have AC3/Dolby audio? The problem might be somewhere else. Maybe you can perform a codec analysis of the files using GSpot, or maybe you can post a sample file here.