Problem

• Java ignores all breakpoints except the first one in the main thread

Solution

• It's a bug in Java 6u14! https://bugs.eclipse.org/bugs/show_bug.cgi?id=279137
• Give the following argument to your JVM:

  -XX:+UseParallelGC
  

• In eclipse you can do this under: Window, Preferences, Java, Installed JREs, edit, Go to Default VM Arguments and enter code above