Same issue in Banshee, Rhythmbox, VLC, and even some (but not all) videos from YouTube, etc. in Chromium. It seems to be strongly related to how many other things are happening on my computer - the more stuff (compiles, lots of apps open, etc.) the more pops. Highly compressed MP3 files seem to be the worst. I even got some short squeals like sliding a needle across a record sideways. It happens with FLAC files just a little bit, but much, much less.
If I open the MP3 file in Audacity, then play, it works as well as a FLAC file. So, I'm getting some popping in the audio stream, but 3-10 times as much when it has to convert from MP3. The FLAC popping settles down after maybe 10 seconds. It still pops maybe a few times a minute for a few minutes before playing perfectly fine (or maybe I get used to a very low level of popping?).
Adding "tsched=0" to the end of the "load-module module-hal-detect" line in
/etc/pulse/default.pa had no effect. I just upgraded to Ubuntu 13.10 - it worked fine in 12.04.
My guess would be a gstreamer or alsa issue, or possibly hardware. If it were hardware, I'd think MP3 vs. FLAC wouldn't matter. I'd also guess it has something to do with not filling enough of a buffer before trying to play the sound. Else why would it get better the longer music is playing?