Well I was reading these messages, and from what I understand the problem is the encoding of the file, or can also be issue in the player.
  Take look, I use a player that helps me manage my music collection, I would recommend to you and test it: http://guayadeque.org, but this player seems some hicups to have run some albums, not only him but also others playes too, such as rhythmbox, for so have other players installed as audacious, sonata, cGMP, quodlibet, etcs
  Each of these has a way to read these, example: dbus, jack, alsa, gstreamer, ffmpeg, ...,  and to my surprise, when an album gets the hiccups at Guayadeque I test with audacious, except in cases of bad encoding the problem is saned.
Secondly, the encoding, ripping can be done in various ways to extract cds, never had problems with asunder, and also the sound-juicer, are simple tools, an excellent tool for ripping soundconverter that is much easier to work for flac, mp3, ogg, and others, is good for between 256 to 320. I have also coded using ffmpeg, lame, mplayer, audacious, there are other tools and other means, but are more complex, sometimes encoding with ffmpeg or anything other can give to u echoes, hiccups or noises, so try use another tool and compare, maybe is a software issue and not a file problem.
There are also sites lowness of which is already ready and encode are always more than 320.
Well, this is a little tips, that i experienced, i expect i could help.

Regards