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hello and welcome
1st. you'll have to choose one and only one to be the master onto which the other will be slave; ok, this IS mostly about timebase, like which one dictates tempo (BPM) and whatever... nevermind...
2nd. while using qtractor 0.9.0 (full transport mode ie.master+slave) and hydrogen 1.0.0beta1 (default config): no issues have been found with jack-transport at least like the ones you report...
so then i'll ask: are you sure all is up to date?
byee