Hi,
I've just wrote a CLI program in C# which can download Smooth Streaming Media and can mux it to MKV.
If you want to test my program. It is available on:
http://dvb-crew.atw.hu/applications.php
it was designed to download streams from
http://www.rtlklub.hu/most/, but its engine is might useful to solve your problems too.
If you can help me, please contact me on MSN:
kissda@primposta.com
Thanks in advance!