I have a recurrent problem with Eclipse: when I try to launch my plugin Eclipse application, it often opens a new tab to "attach a missing source" in jre7\lib\rt.jar. I must be a bug since it usually works and I have never modified that file.
There is a screen of the problem: http://img11.hostingpics.net/pics/436657Bug.png
The only way I found to fix it is to delete the ".metadata" of the project each time it does that... and to loose all my preferences, breakpoints and so.
Keep rt.jar in your classpath. And clean the project.