I finally figured this out. You don't add the files in the inital screen of bbmpeg if all you want to do is Mux. Leaving everything as it is when you open the program, you add no files at all, just go ahead and click Start encoding with the file list blank. When the next dialog box pops up, click settings, and THEN you specify the video and audio files in the Input and Output Files tabs as VS and AS1. Complete the rest ofthe setting and then Click OK and then Start and it will mux.