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Many users are describing a problem they are getting with upgrade from 5.5 or 5.5.1 where the Java DB installation directory is somehow messed up, and they have to reset it using Java DB Database->Settings.
I have searched and searched and can't find any information on how to reproduce this. My apologies for not copying and pasting the emails when I had them. I'll try reproducing blindly, and see if I can hit the problem.
Unable to reproduce. Will re-open if we get a user report of issues.