This has sort of already been reported upstream:
https://bugs.launchpad.net/ubuntu/+source/soundconverter/+bug/792742,
however the conclusion was made that this is instead a problem in
GStreamer and not in Soundconverter. I also tested one of my converted
files with ogginfo and it did indeed produce a similar output.

See also https://trac.xiph.org/ticket/1807 and
https://bugzilla.redhat.com/show_bug.cgi?id=722667. The latter contains
a patch (https://bugzilla.redhat.com/attachment.cgi?id=514575) for
GStreamer which fixes the bug. By compiling gstreamer0.10-plugins-good
from source with this small patch, I can confirm this. Therefore, I am
now marking this bug as invalid, since it wasn't in neither
Soundconverter nor Ubuntu after all.

** Bug watch added: Xiph.org Trac #1807
   http://trac.xiph.org/ticket/1807

** Bug watch added: Red Hat Bugzilla #722667
   https://bugzilla.redhat.com/show_bug.cgi?id=722667

** Changed in: soundconverter (Ubuntu)
       Status: Confirmed => Invalid

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https://bugs.launchpad.net/bugs/796744

Title:
  Regression: Encoding Vorbis from FLAC source causes audible artefacts
  at regular intervals

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