[Just for archive] The menus and contextual menus have incorrect position when JMeter run on GNOME 3 / Java 6 (openjdk or oracle jdk). It's a known issue from Java runtime https://bugzilla.redhat.com/show_bug.cgi?id=698295 A workaround is to use a Java 7 runtime (openjdk or oracle jdk).
Perhaps add to the JMeter release notes ? Probably too late for 2.9, but could be mentioned in the announce and on the website.
*** Bug 56015 has been marked as a duplicate of this bug. ***
This known bug is annotated on Known bugs list on JMeter website: http://jmeter.apache.org/changes.html#Known%20bugs "With Java 1.6 and Gnome 3 on Linux systems, the JMeter menu may not work correctly (shift between mouse's click and the menu). This is a known Java bug (see Bug 54477 ). A workaround is to use a Java 7 runtime (OpenJDK or Oracle JDK). "
This issue has been migrated to GitHub: https://github.com/apache/jmeter/issues/3044