It seems that each planet gets a different bonus from +morale buildings and your race morale bonus when looking at the popup for planet morale. For instance, one planet may be getting 72% morale bonus from my native ability while another is getting well over 280% from my native ability. Meanwhile, neither of them are getting the full bonus from planetary improvements that they should be according to the planet summary.
It seems some of this may be linked to planet population, though not entirely. One planet with a pop of over 35 billion was getting the same 72% from race bonus that a 25 billion planet was getting. Anyone know why all morale bonuses are diminished? It makes it almost impossible to keep planets with a pop of over 15 to 20 billion happy.