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well, yes, it seems a hydrogen problem - just checked out hydrogen svn and problem persists.

both qtractor's playhead and qjackctl's bar number behave as expected. I noticed now that it suffices to pause and resume playback (either in h2o, qtractor or qjackctl) to have the playhead in hydrogen jump around, i.e. when I resume playback about 50% of the times the playhead jumps somewhere else in the track and plays from there.

so I'll be reporting it to hydrogen devs...

EDIT: link to post on h2o forums

thanks
renato