This certainly is a bug of Quarry in Ubuntu.

I have done a clean install of Dapper 6.06 with Quarry and GnuGo in
order to verify it.  This was a completely default install, and the
Quarry package from the Universe respository.  The error is there, and
it is replicable.

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Quarry forgets preferences
https://launchpad.net/bugs/54401

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