While progressing down the Benevolent Ideology tree I chose Benevolence, Pioneering, Mindfulness, and Breakthrough. After each of those choices, the number of points I had accumulated (shown in the upper left corner) was decremented by the number of points required for each choice.
However, on my next choice, I had 52 points available, I chose Empathy, and afterwards I still had 52 points.
There's a saved game here. Since it was saved after I made my choice of Empathy, I'm not sure that it will tell you anything. But it does exhibit another strange behavior - if I open the Ideology window, and do nothing except click on Done, it automatically opens the Technology window.