This may or not be the fix. There was no traffic on the feed, so I couldn't hear what you're talking about.
I've noticed that when I use the output to feed amplified speakers, there was a "pounding noise", so I used an old paging transformer to isolate the output. I built the transformer into a pill bottle, making a compact in-line filter. I think you get the idea.
This information comes from another post:
"You might try adding an isolation transformer between the radio audio and the input to the sound card. Radio Shack Part # 273-1374 (1:1 turns ratio audio isolation transformer)."
Does the clicking occur through the speaker on the scanner, or just when the output is connected to your sound card?
I'm sure now that I have started the discussion, a vigorous discussion and debate will ensue over the next several months, about part numbers, specifications, ground loops, sound cards, firmware, software, mini connectors, solder and shielded cable.
Hey, that's why we're here, right?