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.
-- Quarry forgets preferences https://launchpad.net/bugs/54401 -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs