I updated to the newest alpha yesterday, and discovered that one of my planets with over 300 atms of pressure, which usually is over 3000 C is now below freezing. It appear that no matter how thick a planet's atmosphere, it doesn't seem to have an effect on the planet's actual temperature. Planets always seem to cool down to their effective temperature. Even in the simulation of our solar system that first pops up when the game is loaded, Venus rapidly cools down to around -77 C. The greenhouse effect stat seems to work like normal, but doesn't seem to factor into the planet's overall temperature. Manually modifying the greenhouse effect updates the planet's temperature to around where it should be, but then it immediately starts to drop back down to the effective temperature.
In a similar vein, the temperature of newly-placed gas giant planets is inconsistent. Sometimes a gas giant placed 100 AU from a star can be moved less than 0.1 AU from that same star and hardly warm up at all, and other times moving a gas giant near a star can cause the gas giant's temperature to wildly fluctuate around an average of 0 C.
Given that the previous alpha's problem of planets being unable to display temperatures above 5000 K has been solved, I'm inclined to believe that this issue is a bug that resulted from that fix.