I had problems that some break points did not take in my Eclipse 3.4.1 when I updated from JDK 1.6 update 12 to JDK 1.6. update 14. Well some breakpoints took, but none in the AWT thread. It could be a coincidence, I don't know.
I updated to Eclipse 3.4.2 but that did not solve the problem.
I had to downgrade to JDK 1.6 update 13 to solve the problem. It was enough to choose another JDK for my specific project. Eclipse itself could run update 14.
I searched the Internet but could not find any official bug either in Java or Eclipse. Anybody out there got more information?
Update: the problem is now fixed: http://blog.lesc.se/2009/09/jdk-breakpoint-problem-fixed-in-update.html