As mentioned in another thread, the Touchpad-configurator settings using syndaemon tend to disappear after a logout/login.
Adding the settings made by TP-configurator to ".e16/startup-applications.list" gets it back every time but I doubt @Thanatermesis intended it to work that way. 
mmmh, yeah, "startup applications" are meant all of them to be closed after finishing the graphical user session, and started up again after to login
this is meant to be a good and expected thing that won't give any problems
by other side I don't think syndaemon is related to this, maybe its just closed by itself because the graphical session finished