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By default, eXist creates its data directory in EXIST_HOME/webapp/WEB-INF/data. On windows, this means that the data dir is located below the Program Files directory. While this is usually ok for Unix (Apple?) users, Vista doesn't really like it when users are writing data into Program Files (it creates a shadow dir if you are not an administrator).

The installer should ask for an alternate location for the data directory, maybe depending on the OS type.