So, having played with things a little more. It seems like it's just not possible to get the skill points option to work on your first level up. However, after I leveled up a second time I was able to change the amount of skill points to spend. The number for ability and skill points still jumps back and forth in the editor, it's weird, but you can change the skill points as long as you have already actually spent a skill point on first level up.
Oh okay I didn't know that about the skillpoints as I first tried the option on my second level up. Yeah I saw the numbers for XP, skill points and ability points go up and down all the time,