They probably have that set as the default setting as most organ sounds don't use much if any sustain unless you're going for that old schmaltzy Lowrey organ sound. I'm quite certain if you just go to where you modify the voices (voice edit) you'll find you can adjust the sustain to where you want it and then save it as a user voice. I had experimented doing that with a piano sound a while back using different settings for reverb and sustain to make it sound better in rooms that have dead acoustics.
I just reread your post, I missed the part that you are using the sustain pedal, I thought you were using the sustain button. Don't know on that, because it's not really a typical organ sound, it would be like using sustain on an accordian. Course you might get some cool effects you like doing it.
[This message has been edited by Scott Langholff (edited 10-06-2009).]