I have had this problem for a long while as well, and just found this
bugreport which does not seem to help at all. Now I just found that the
skipping happens because of the fact that faac's default encoding
profile (MAIN) seems to encode or at least play back with
jitter/skipping. Switching to the profile to Low Complexity (fast) or
Long Term Prediction (slow) seems to fix it. (profile 3, Scalable
Sampling Rate, makes sound-juicer fail).

I will be using the following gstreamer pipeline from now on:

audio/x-raw-int,rate=44100,channels=2 ! faac bitrate=256000 profile=2 !
ffmux_mp4

(other options for faac can be found with "gst-inspect-0.10 faac";
testing pipelines can be done by starting sound-juicer from commandline
and seeing the error-messages when sound-juicer tries to initialize a
pipeline)

cheers,

-- 
sound juicer aac formatted files skip and...
https://bugs.launchpad.net/bugs/95326
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