Two days ago I had a problem when configuring the ADC Periodic Framework using the Synergy Configuration tool. I tried to acquire simultaneously some normal analog channels plus the internal temperature sensor value and it resulted in an run time error which, as Karol pointed, is because an incompatibility listed in the written documentation of the SSP.
My suggestion is that, in the same way it is done with the pin assignments, all the known peripheral incompatibilities should be taken into account by the Synergy Configurator and warn the user, otherwise one of the main advantages of using the configurator is lost, because we also have to read very carefuly every single line of the documentation before changing the properties of a driver or a framework.