ForceofNature i checked... and it's a problem of coding flow.
hidden scores increase for orc evolution are applied the moment you select the choice, not during the next iteration like strength, intelligence and discipline. but for yhilin govern I it's happen before i set orc stats based on unique orcs you have. so the change are applied... only to beign overwritten few lines of code after.
fixing is trivial, but at this point i don't know when i will be able to release an update, and with an high probability will include 0.59.* content.
for a quick workaround you can delay the orc evolution in yhilin II section (no check are made before that).