Well like I said, using the batch file that came with the encoder, and just changing the settings, it encoded just fine. VBR worked and sounded good. But not gapless.

And as for listing the tracks to be encoded, at least with 3.92, in my experience, if you type TRACK01.WAV TRACK02.WAV TRACK03.WAV, the first track will be saved over the second track as track02.wav, but it's really an mp3, and then the second track (now a copy of the first as mp3) will get saved as track03.wav, but also really an mp3, and then you will have track03.mp3, an actual mp3. But because of all the copying, all of these files will be the same track.