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It looks like instrumentation filter passed to RecursiveMethodInstrumentorXX classes is different from the one you specify in the IDE (and is actually always a "None" filter). Probably this has something to do with ProfilerEngineSettings management (filter isn't copied into it or something). To check, try to run some simple project with standard "exclude Java core classes" filter.
It seems that calibration is resetting certain ProfilerEngineSettings. This was likely in M6. Fixing in M7
old issue, closed