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well, a year ago, iirc. qtractor and hydrogen were more finicky re. jack transport positioning--not anymore, at least on the qtractor side :)

anyway i've just tested with hydrogen 0.9.6svn trunk and it doesn't show any of the behavior you're reporting.

care to try again or please explain in more detail what seems to be the problem?

which of the programs (qtractor, hydrogen or even qjackctl if you happen to be running it too) shows a wrong transport position (time) ? from the above report it seems it's hydrogen but i repeat i could not reproduce the issue with the latest svn trunk.

cheers