OK, I found it.
So, it was in: src/engine.cpp, around line 1674, you had a hack (I don't know why, I suppose there is a reason, but I coudln't figure out whichi one) like:
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bool flag = gs_event->value > 0.0f;
if (_driver->set_timebase_master(flag)) {
_jack_timebase_master = flag;
} else {
_jack_timebase_master = false;
}
I just replaces those lines by the following one:
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_jack_timebase_master = gs_event->value;
I also had to change something in src/gui/latency_panel.cpp, as timebase_master was once set to globals variable, and then to control. So here it is, replace this line:
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lcontrol.post_ctrl_change (-2, wxT("jack_timebase_master"), _jack_timebase_master_check->GetValue() ? 1.0f : 0.0f);
by this one
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lcontrol.post_global_ctrl_change (wxT("jack_timebase_master"), _jack_timebase_master_check->GetValue() ? 1.0f : 0.0f);
(for this last hack, I'm not sure it's absolutely necessary, but I think it may).
And it worked. Though, it doesn't check the box in GUI. It seems to be hard coded that it is set to uncheck, even if timebase master is set (in latency_panel.cpp, if I'm not wrong).
Hope it helps, and hope I'm not wrong.