turns out it was a problem with the bugs in X2Pro LE Audio Converter 3.0.4. BUT… I emailed them and they are waiting on a newer version of the software (3.0.5) to be posted to the App Store that fixes the bugs. But they sent me a beta version of 3.0.5 and it worked just fine. They were super helpful about it.
Thanks, Eric, for inquiring about my problem. All of my files are WAV sound files, and all of my video are QT files. Seems simple, right? But it all worked out! How often can you say that something like this gets resolved within 24 hours?