I suspect this is a known pilot-link bug, present in version 0.12.2 and 
scheduled to be fixed in the 0.12.4 release.
  http://bugs.pilot-link.org/1872

You can check whether this is the problem by running gpilotd in a
terminal window.  If you see a segfault after sync then this bug is
likely the cause.

It should be straightforward to patch using the diff attached to the
above bug listing (fedora have been using the patch for over a year).

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Gnome-Pilot Bluetooth HotSync Functions ONLY Once without "device" re-mapping
https://bugs.launchpad.net/bugs/373507
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