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Really glad to hear you found them!
I think this question might point you in the right direction: https://stackoverflow.com/questions/4947555/where-are-the-java-preferences-stored-in-windows-7 I think FreeGuide uses the user preferences, which means you are probably looking for HKEY_CURRENT_USER\Software\JavaSoft\Prefs . (The relevant code is at https://github.com/andybalaam/freeguide/blob/deb611749ea0bacd3b9d0158709312001f65ed65/src/freeguide/plugins/program/freeguide/FreeGuide.java#L238 )