If "Java version for Javadoc links" is set to 1.6, the links do not generate. It works for 1.5, but not for 1.6. I even found the line that needs to be fixed:
In the method _getLinkArgs() in the DefaultJavadocModel, it only handles versions 1.3, 1.4, and 1.5. It looks like another line needs to be added to support 1.6.
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Thanks, this was my oversight when I extended the Javadoc features to 1.6.
Fixed as of revision 4637.