I figured out something interesting: If you enable the mixer via 'Choose View > Show Mixer (or press X)' in logic, then the faderport keys work. So after I load my project I have to enable the mixer via the 'x' key (not the external mixer window!) ... than logic is stable with the keys in faderport.
You have to do this only once. After you close the mixer again, faderport still works as expected.