I had 245 spirit energy and 69 regen per hour at level 12 and raised my int by 1 and Fountain of Spirit skill by 1 from 3 to 4 (which should have given me a +21.5 total regen per hour boost) Instead I only received a +11.5 total regen per hour boost.
Fountain of Spirit skill is supposed to go from +20 per hour to +40 per hour when one goes from 3 skill slots to 4 skill slots in it.