FFMPEG 0.8.9 audio recording causes clicking sounds
 

Whenever I'm recording a screencast using FFMPEG on Fedora 16 with pulseaudio I keep getting an annoying clicking n the background. The clicking does not exist in other audio recording programs, just ffmpeg. Is there any way I can eliminate this clicking?
FFMPEG command:
The clicking sounds a bit like static, but as I said, I've eliminated the possibility of static.

Have you tried to use another codec for your mkv audio?

I'd guess the system is having a hard time with the work. Run top when you do this maybe.

Other codecs give the same issue.

The system isn't working too hard with the encoding. CPU usage for ffmpeg is detected as 150% using top and "system monitor" detects that each CPU core is not going above 60% when I am running it. I have ffmpeg set to use 2 threads, but this also happens if I give it 4 threads (and uses the same CPU percentage).

First of all make sure that is an encoder problem and not a decoder issue: try to open the created file on another machine and check if the sound is still "clicking".
As second step try to use another format (not mkv) as mpeg or mp4 keeping the codecs so that you can say if the issue is related to the container and not to the codecs.