Sorry, I got no helpful info for you...though it sounds like you have more than one issue: pops, beeps and what sounds like "arm-pit farting."
I've found that on rare occasions when I don't stick the optical all the way in the NJB3, I might get some pops...while I wouldn't circulate the show, for my own listening pleasure I might run it through SoundForge (7.0) in Vinyl Restoration. Usually that removes the pops or, at least, minimizes them so I can tolerate listening.