Hmmm... I remember this being discussed some time ago. Did you try to do a search in this forum?
Anyway, the only workaround I know is to change the default settings for Quicktime in Shake.
Simply create a .h file in your include/startup directory with the following text:
sys.QTDefaultSettings =
"100W@u3000WDcsuHA#M000E@4J3In8q5CBRZ0VY2LKKPgATB3A9KSC7gXaC30q8v
W16OG5Koq10h2A5HIvi00ieKA9WT6a1rS9hH8dqIEiBqOHT0SJEZ8HHc8qtf4rlxS
AP9WYwcYJHfMMCKpWXYn2W893LCsk080000@00000000000;";
The long string here should be replaced with the one that holds your codec definition.
Now if you -fo to Quicktime from the command line, this will be the default codec.
Hope that helps.