... ok, you have real a HD Installation of Knoppix on /dev/sda3. Therefore I cannot understand, what you mean with
To my suprise after installing and configuring a reboot wiped out all my changes.
What had been "wiped out"?

But what's about /dev/sdc1? Is there also a Knoppix installation? Perhaps flash disk installation?

Greetings Werner * http://www.wp-schulz.de/knoppix/summary.html
Own Rescue-CD with Knoppix (Knoppix V6.4.4 remaster)