What I found was it was assigning level-valued slots to the inherent powers, thus preventing you from physically placing slots from level 3.
That is, you would start a new hero/vill and then pick your level 1 and 2 powers, but then it wanted you to pick your level 4 power immediately after that. Then you could place the two slots from level 5.
Did not notice until a while later. Still, I whole-heartily recommend funding these guys, as without this planner, I would probably not play CoH all that much anymore. It's just that good.
-r0y