For a long time I've had a hit and miss relationship with debugging in MyEclipse. I'd set a breakpoint, cross my fingers and hope it would stop at that point. About 80% of the time it would. The other 20% was a real pain in the butt.
Finally decided to sort it out once and for all and it turns out to be a bug in the jdk 1.6.0_14 I'm using.
All you need to do to fix it is add -XX:+UseParallelGC to your jvm arguments.
Window -> Preferences -> Java -> Installed JRE's -> (edit your currently used JRE) -> Edit "Default VM Arguments" box and enter (w/o questionmarks) "-XX:+UseParallelGC"
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