I found a sweet little plug-in to take care of all the pops. Waves X-Crackle. It removes obvious pops without ruining any of the original source. To check it, you can easily hear only what you remove to make sure you're not taking out to much.
X-Click seems to work also, but not as easily.
Also, looking back (since it's been three months since this thread has been active) the problem was that my jb3's optical input was bad. Since then I've acquired a new jb3.