Hi Daniel,
Saw your earlier message about this and meant to get back to you- Ive never seen this before, but I suspect its the Jack library printing out all of this, which is somewhat poor form. I think the way OS X audio works is that it loads every possible audio driver when you ask about available audio I/O endpoints, which then gives Jack the opportunity to print out all of this.
Depending on if these messages go to stdout or stderr you could suppress them by redirecting those with 1> /dev/null or 2> /dev/null at the end of your chuck command. This is not great though because if the Jack messages go to stderr you wouldn't get any of the normal internal logging messages from ChucK, or compile/run-time errors. You could still print from ChucK code using chout or cherr depending on which one of these you suppress.
Or maybe Jack has a way to configure it to be less verbose.
spencer