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And which Qtractor version? tempo? time-signature?

Try disabling the MIDI metronome and retry with the audio metronome enabled. Try with some short but distinct bar and beat audio sample files. See (hear) whether the strange patterns you report occur as bad.

On all my tests with released 0.3.0 and latest CVS, both metronomes work as designed (ie. no bugs found;) Maybe I'm missing something ... it happens all the time :))

Seeya