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It seems that the bookmarks module configures the settings twice, once directly and second time through SettingsInitializer. Generally, the ModuleInstall is quite compilcated :-(
Yes, it should be enough to add the settings from the initializer.
Removed the duplicate code and also some other Settings related mystery code in the finish() method. Checking in EditorBookmarksModule.java; /cvs/editor/bookmarks/src/org/netbeans/modules/editor/bookmarks/EditorBookmarksModule.java,v <-- EditorBookmarksModule.java new revision: 1.7; previous revision: 1.6 done