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Rui,

here are the results:

1: The problem IS connected to the FireWire device. I when I test with my Delta 44, there does not seem to be this problem.

2: Debug-Output
I did as you told me, started the song with all midi tracks muted and activated the MIDI tracks one by one. See log below
(Everything after *** are my comments)

3: After I have seen theese sendAllControllers(0) immediatly before the problem, I commented it it out in the source and recompiled. It does not solve the problem but prevent if from occuring immediatly.

Here we go:

*** Starting qtractor

Warning: no translation found for 'de_DE' locale: /usr/share/locale/qtractor_de_DE.qm
qtractorPluginPath[0x7fff39699ff0]::open() paths="/usr/local/lib64/lv2:/usr/lib64/lv2" typeHint=4
qtractorLv2PluginType::slv2_open()
librdf warning - Model does not support contexts ( *** 3 times ***)
qtractorMainForm::loadSessionFile("/home/dehnhardt/QTractor/Default Session.qtr", 1)
qtractorMainForm::updateSession()
qtractorMidiManager::createMidiManager(0x2f4ba30)
qtractorMidiManager::createMidiManager(0x7f9b90000d30) *** 9 more addresses

--snip

qtractorMidiEngine::resetDrift()
qtractorMidiManager::createMidiManager(0x7f9b9026c5a0) *** 4 more addresses

--snip

qtractorMainForm::viewRefresh()
qtractorAudioBus[0x2ee8ad0]::updateConnects(1): jack_connect: [firewire_pcm:000ff20400001d98_Unknown_in] => [Qtractor:Master/in_1]
qtractorAudioBus[0x2ee8ad0]::updateConnects(1): jack_connect: [firewire_pcm:000ff20400001d98_Unknown0_in] => [Qtractor:Master/in_2]
qtractorAudioBus[0x2ee8ad0]::updateConnects(2): jack_connect: [Qtractor:Master/out_1] => [firewire_pcm:000ff20400001d98_Unknown_out]
qtractorAudioBus[0x2ee8ad0]::updateConnects(2): jack_connect: [Qtractor:Master/out_2] => [firewire_pcm:000ff20400001d98_Unknown0_out]
qtractorAudioBus[0x2e66ab0]::updateConnects(1): jack_connect: [firewire_pcm:000ff20400001d98_Unknown_in] => [Qtractor:Mackie 1/in_1]
qtractorAudioBus[0x2e66e60]::updateConnects(1): jack_connect: [firewire_pcm:000ff20400001d98_Unknown_in] => [Qtractor:Mackie 2/in_1]

*** Naming of the ports is not finished in ffado, therefore these 'unknown...' names

qtractorMidiBus[0x2e67720]::updateConnects(1): snd_seq_subscribe_port: [130:1:Master] => [20:MTP direct 8]
qtractorMidiBus[0x2ee9890]::updateConnects(2): snd_seq_subscribe_port: [130:2:K2000] => [20:MTP direct 2]
qtractorMidiBus[0x2eea040]::updateConnects(2): snd_seq_subscribe_port: [130:3:P30] => [20:MTP direct 8]
qtractorMidiBus[0x2ee9890]::setPatch(9, "Kurzweil K2000", 0, 0, 4)
qtractorMidiBus[0x2ee9890]::setPatch(1, "Kurzweil K2000", 0, 0, 6)
qtractorMidiControl::sendAllControllers(0)
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3

*** Load Song

qtractorMidiManager::deleteMidiManager(0x2f4ba30) *** 14 times

-- snip

qtractorLv2PluginType::slv2_close()
qtractorMainForm::loadSessionFile("/home/dehnhardt/QTractor/Clicky Neu/Clicky Neu.qtr", 0)
qtractorLv2PluginType::slv2_open()
librdf warning - Model does not support contexts *** 3 times
qtractorMainForm::updateSession()
qtractorAudioBuffer[0x302cc70]::seek(151200) pending(0, 151200) wo=282271 ro=1537181
qtractorAudioBuffer[0x30a6320]::seek(302400) pending(0, 302400) wo=433471 ro=1884489
qtractorMidiManager::createMidiManager(0x2e24770) *** 10 times

-- snip

qtractorMidiEngine::resetDrift()
qtractorMidiManager::createMidiManager(0x7f9b9037ddb0) *** 4 times 

-- snip

qtractorMainForm::viewRefresh()
qtractorMidiBus[0x3021f90]::updateConnects(2): snd_seq_subscribe_port: [130:3:P30] => [20:MTP direct 8]
qtractorMidiBus[0x3087c40]::setPatch(9, "Kurzweil K2000", 0, 0, 84)
qtractorMidiBus[0x3087c40]::setPatch(9, "Kurzweil K2000", 0, 0, 84)
qtractorMidiBus[0x3021f90]::setPatch(0, "", 0, -1, 0)
qtractorMidiControl::sendAllControllers(0)

*** Song loaded -> play

qtractorMainForm::transportPlay()
qtractorMidiEngine::resetDrift()
qtractorAudioBuffer[0x302cc70]::inSync(0, 128) (0)
qtractorAudioBuffer[0x30a6320]::inSync(0, 128) (0)
qtractorMidiEngine::drift(): iAudioTime=7841 iMidiTime=7833 (8) iTimeDrift=8 (0.1%)
qtractorMidiEngine::drift(): iAudioTime=28002 iMidiTime=28013 (-11) iTimeDrift=-3 (-0.012%)
qtractorMidiEngine::drift(): iAudioTime=38086 iMidiTime=38094 (-8) iTimeDrift=-11 (-0.029%)
qtractorMidiEngine::drift(): iAudioTime=48164 iMidiTime=48169 (-5) iTimeDrift=-16 (-0.034%)
qtractorMidiEngine::resetDrift()
qtractorMidiEngine::drift(): iAudioTime=27040 iMidiTime=27039 (1) iTimeDrift=1 (0.0031%)
qtractorMidiEngine::drift(): iAudioTime=37124 iMidiTime=37123 (1) iTimeDrift=2 (0.0046%)
qtractorMidiEngine::drift(): iAudioTime=47202 iMidiTime=47199 (3) iTimeDrift=5 (0.0092%)
qtractorMidiEngine::drift(): iAudioTime=57285 iMidiTime=57282 (3) iTimeDrift=8 (0.014%)
qtractorMidiEngine::resetDrift()

*** Now unmuting a first MIDI Sequence

qtractorTrack[0x3217800]::stateChangeNotify(1, 0)
qtractorMidiEngine::trackMute(0x3217800, 0)
qtractorMainForm::contentsChanged()
qtractorMidiEngine::drift(): iAudioTime=5923 iMidiTime=5921 (2) iTimeDrift=2 (0.034%)
qtractorMidiEngine::drift(): iAudioTime=16000 iMidiTime=16002 (-2) iTimeDrift=0 (0%)
qtractorMidiEngine::drift(): iAudioTime=46246 iMidiTime=46244 (2) iTimeDrift=2 (0.0031%)
qtractorMidiEngine::drift(): iAudioTime=56323 iMidiTime=56322 (1) iTimeDrift=3 (0.0046%)
qtractorMidiEngine::resetDrift()
qtractorMidiEngine::drift(): iAudioTime=4961 iMidiTime=4958 (3) iTimeDrift=3 (0.06%)
qtractorMidiEngine::drift(): iAudioTime=15045 iMidiTime=15048 (-3) iTimeDrift=0 (0%)
qtractorMidiEngine::drift(): iAudioTime=25122 iMidiTime=25124 (-2) iTimeDrift=-2 (-0.0092%)
qtractorMidiEngine::drift(): iAudioTime=35206 iMidiTime=35207 (-1) iTimeDrift=-3 (-0.0092%)
qtractorMainForm::contentsChanged()
qtractorMidiBus[0x3087c40]::setPatch(9, "Kurzweil K2000", 0, 0, 84)
qtractorMidiBus[0x3087c40]::setPatch(9, "Kurzweil K2000", 0, 0, 84)
qtractorMidiBus[0x3021f90]::setPatch(0, "", 0, -1, 0)

*** Start of sequence!

qtractorMidiControl::sendAllControllers(0)
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3

*** What does this mean??? Here the timing is already instable

qtractorMidiEngine::resetDrift()
qtractorMidiEngine::resetDrift()
qtractorMidiEngine::resetDrift()

*** activating a second track

qtractorTrack[0x30c0470]::stateChangeNotify(1, 0)
qtractorMidiEngine::trackMute(0x30c0470, 0)
qtractorMainForm::contentsChanged()

*** and now everything gets out of sync.
*** What does JackActivationCount... means?

JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3
qtractorMainForm::transportStop()
JackActivationCount::Signal value = 0 ref = 3
JackActivationCount::Signal value = 0 ref = 3