Subj.
Steps to reproduce:
1) Take any jar with classes that are present in JDK (for example, JDK 6 and JAXWS or JAXB API)
2) Add this jar to project with specified JDK
3) Open Go To Class menu (CTRL+N)
4) Type class name
5) You'll get only one result that is from JDK.
However if you have duplicate classes in jars (and not in JDK) then you get multiple results which is expected.