You might not have much luck getting this question answered in a time where Xcode 4.4 just went GM and is ready to submit apps. Xcode 3 is really old and has it’s fair share of problems. Time to move on.
To be fair, even in Xcode 4 breakpoints are not always working. But LLDB got a lot better and is pretty reliable now.
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solved Breakpoints not Working in Xcode 3.2.5 [closed]