Hey there, I had the same problem and I solved it completely (even with my noisy SB16!), so I'll gladly post this answer which I hope will help all those with the same doubts. Here are all the steps I followed to get rid of the clicking noises.
1.- I unplugged every single electric stuff that might be in my room, such as the TV, lamps, etc. It might not be necessary, but when I'm going to process the clicking noises, and just in case, I even disconnect my self-powered speakers. You could just do the same...
2.- Again, when the time comes that you're going to process the noise from your files, check up the windows mixer (sorry here if I make some mistake but I've got windows in norwegian), be sure you uncheck any line-in, cd-in or whatever (no dirty signals going in) and that nothing except the dispositive you use to listen is plugged to your soundcard. Of course all this might be unnecessary, but you just asked me the way I do it!
3.- When I posted my question in audioforums.com, I got an answer from a one Roy (cheers mate). He plainly told me to visit these two faqs in syntrillium, very helpful both:
support.syntrillium.com/faqDetail.html?4 support.syntrillium.com/faqDetail.html?37
4.- Okay, if you followed the steps above you should notice a lot of improvement by now, but still get one or two clicks somewhere, right? Then here goes the good one. I didn't know this for a couple of days ago, so you've been lucky to ask me. Get your file, go to CEP and retouch and clean it as you want. Save it with 'save as...' or whatever. Now, close the file, open it again to check if there are any clicks (listen to it carefully). If there are none, good, you've got it. If there are some, just select the small area where the click is an eliminate it. Then save with the 'save' command (not 'save as...'), and you'll see that it only saves the small part of the file you have retouched! That means, less working space, less new noises produced! It won't touch the rest of your file, only the part you retouch. This is a fantastic feature, no doubt.
5.- Almost last advice: if you're using the syntrillium's included noise reductor, drop it, it really sucks. I would recommend you to go out there and get yourself the clickfix2000 plug-in, fast and the best I've seen. If you've got a fast connection I could even send it to you, it's very small.
6.- Another last advice. Sometimes you check the noises with cool edit and find none, but when when you go to Cakewalk there are. First, don't check the files with cake, do it with something like winamp. Its drivers will REALLY tell you if there's some noise. I there are none in winamp, then go to cake and insert the file again, it was probably a problem on reading. If it keeps, try again. It won't take more than a couple of tries to get it clean in cakewalk.
7-. Once you mix or whatever you do with cake, I would recommend to go back to CEP and process the file for the final cleaning. Haven't done it yet, though. As I told you I'm still working with it!
Okay, that should do it. Hope you get it right and just feel free to e-mail me if any doubt should come (as long as I know about it!). Bye.