To make the DivX Converter see and convert your video's 5.1 surround sound audio instead of 2.0 stereo you will need to configure your ac3filter or ffdshow decoder output settings. By default the output settings in these filters are set to stereo. Once you change the output to the correct option as listed below and re add the file to the DivX Converter you will now see your video's 5.1 surround sound.
Please Note: If your file does not have a 5.1 surround sound audio stream then this will not change.
To do this for AC3 DirectShow Filter, open your Start menu and select All Programs, then open the AC3 Filter menu and select "AC3 Filter Config". In the AC3 Filter Config window, under the Main tab, you'll see that the Output format is 'Stereo'. Use the drop-down menu for Output Format and set it to "Do not change":
If you are using FFDShow, go to Start menu > All Programs > ffdshow and select Audio Filter Configuration. Select 'Mixer' and then in the Output Speakers Configuration dropdown menu, change to "same as input":