that is really odd because as you can see in my first system I have the exact same setup and all of my mpeg2 recordings are in 48 khz. Have you tried any other encoding software like, tmpgenc or (damn i cant remember its name

there is a thread in the support forum about mpeg audio sync issues that names some other encoding programs but its late and I cant think of any off the top of my head). You might want to check the log files and make sure that snapstream is saying the audio is being recorded at 48khz if the logs say this but the file is otherwise then there might be an issue with snapstream.
Intervideo might not be using your sound card at 48khz but instead taking the live stream from it and resampling to 48khz when it encodes to mpeg. Snapstream can only record audio in formats that the audio card supports
you might want to try updating the drivers on the card to the latest