I recently ran into a weird issue. I had to debug a piece of code that I wrote. So I launched the application in Eclipse in debug mode, and set a few break points. Though I can see that the log messages related to all the break points appear in the log, it didn't stop in all the break points. In some break points it stopped and in some other it didn't stop. I checked the output directory, I checked the flags to the compiler, even I downgraded to Ganymede. Nothing seemed to work.
When I asked the question in the stackoverflow.com, I got the answer in five minutes. Looks like JDK 1.6 update 14 has an issue with debugging. So upgrading to JDK 1.6 update 16 helped. But still I am seeing the issue occasionally.