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With JDK6 U12 the project properties for a NetBeans Platform Application does not show the checkboxes under "Project Properties > Libraries". The check-boxes are available and can be clicked, but the clicked state is not visually represented. Dropping back to JDK6 U11 fixes this issue. I have tested this issue with Windows XP SP3 and Windows 7, both with the current daily build (200902061401) and 6.5.
The same root cause as issue #157300, should be resolved with the fix. *** This issue has been marked as a duplicate of 157300 ***