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i've read the explanations and i don't buy them :)

jack transport absolute position is primarily expressed in frames, not in musical metrics (bar.beat.tick aka. bbt).

hydrogen should read and convert that position (in frames) to its own metrics (in bbt) even though qtractor does supply its own conversion as a transport master. iow. hydrogen shouldn't rely on the bbt information supplied by qtractor when it has a song metric (beats per bar) and/or resolution (ticks per beat aka. ppqn) of its own.

i guess that's the root of the problem: in general, all sequencers participating in a jack transport session should agree to follow the tempo, bbt position and resolution of the master. otherwise they should just follow absolute transport frame position, no less.

hth.
cheers