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Pop info message is: The chosen operation is not enabled. Follow steps in http://dev.eclipse.org/help21/index.jsp?topic=/org.eclipse.platform.doc.user/gettingStarted/qs-52.htm to setup for compare and then http://dev.eclipse.org/help21/index.jsp?topic=/org.eclipse.platform.doc.user/gettingStarted/qs-52.htm to do compare.
Which version of Eclipse are you using? In 3.0 M1 we had bug #38713 which has been fixed in recent builds.
*** This bug has been marked as a duplicate of 38713 ***