I've had a long-standing problem with hydrogen's Jack output, where the notes sound clipped or badly aliased (sounds similar to a period mismatch). I will detail the problems and then a quick and dirty workaround that solves them.
Starting hydrogen with "--driver jack", or "jack"/"auto" output selected in preferences and just running hydrogen with no options results in:
1) Two jack outputs being created "hydrogen-1" (which has no sound output) and "hydrogen-2" (which has sound output).
2) The resulting sound is terrible (I tried to attached a .ogg but the forum software won't allow it). Note lengths are also shorter. If you record the "GM_kit_demo_1" it will be about 1 second shorter than normal.
3) The following is output to the terminal during startup:
(E) void H2Core::audioEngine_init() Error the audio engine is not in UNINITIALIZED state
(E) void H2Core::audioEngine_startAudioDrivers() The audio driver is still alive
(E) void H2Core::audioEngine_startAudioDrivers() The MIDI driver is still active
(W) static QString H2Core::LocalFileMng::readXmlString(TiXmlNode*, const QString&, const QString&, bool, bool) 'license' node not found
(E) void* H2Core::alsaMidiDriver_thread(void*) seq_handle != NULL
My quick solution:
1) Open hydrogen and in preferences select the "Auto" sound driver. (Do not select "Jack"). Close hydrogen so that the preferences are saved.
2) Start hydrogen with the '--driver alsa' option.
3) Open preferences and click "restart driver"
Now hydrogen+jack work as expected.