I am also having the same problem (but only recently).
This started when I tried ripping CSI Season 4 (all discs).
My normal process is to rip the dvd to hard drive using DvdShrink 3.2. This gives me an unencrypted file system to rip from, and allows me to queue up all the rips at once.
Then I was transcoding with Dvdfab 126.96.36.199 as a Generic avi xvid mp3 with the mp3 as 192kbps 105% volume. Fixed bitrate of 1000kbps 704x400 framerate same as source. I got the same beeping/popping noises as was described in this thread.
I re-ripped the discs to hard drive using DVDfab to see if that fixed it. It did not. I am relatively sure the source files do not have this noise as PowerDVD did not have the audio noise. Next I upgraded Dvdfab to 188.8.131.52 and still the same results.
I tried lowering the volume to 100% and the pops got weaker, but still there. Volume was too low for my liking.
I tried using audiocopy and they were not there as far as I could tell, the audio volume was just too low for my liking.
I tried generic avi h264 mp3, and the same avi xvid mp3 at different bitrates (still 105% volume) and got the same result.
I prefer my generic avi xvid mp3 as it gives good quality (pc playback) and I can increase the volume slightly so it is more on par with my other video and music.
Any suggestions would be appreciated.