SQL Developer starts every time as if first time and ingores preferences

Every time I launch SQL Developer, it offers me to configure file type associations. Also, many preferences, such as tab settings for editor, while preserved between sessions, have no effect. Other settings, such as the interface style, work normally.
Windows Vista Business 32bit
SQL Developer 1.2.1 Build MAIN-32.13

The file associations thing means you don't have access to the registry to associate file types. Probably connected to the Vista security model. Try registering the filetypes for use by sqldeveloper through explorer.
This other problems generally means you don't have write access to the sqldeveloper system directory.

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