This is from a new player, trying to learn the game. To begin with, it can be a bit confusing trying to remember what setting you saw where. You know you saw it somewhere, but you don't quite remember where. Was it under a director? Was it under the governor?
The problem is this Pay-Per-View system where you can't see the screen with the settings without paying political points. It can be frustrating to a new player to pay to enter a screen, then to realize that the setting they wanted to adjust isn't even on that screen. I'd imagine this goes away with time, but for a new player it can be frustrating.
To keep it simple and not effect the balance of the game, you could just move the 2 PP cost to the button that 'Confirms' the changes. It still costs 2 PP to adjust the priorities, but you don't have to pay it in advance.
Sometimes in the game these settings seem to come up for free. That could still happen. Its just on those occasions, for instance in a government yearly scheduled budget process, the player is told that this time there is no 2 PP cost for adjusting the budget. Or you could keep it simple and just say that changing the budget always costs 2 PP on the Confirm button. Even if its an annular process, just adopting last year's budget again is usually politically easier than making changes.

----------
Another suggestion along the same lines of helping new players trying to understand this multilayer system.
The game does a good job of using Tooltips in places to provide information to the player. The National Budget Adjustment screen would be a good place to use these. A new player is trying to remember just what the Interior Council does or the Staff Council. A tooltip that tells what these BP could be used for in that council would be very helpful on the sliders of the Budget Adjustment screen.
The sort of thing that reminds that that Economic Council has under it four areas, Strategem Discovery, Strategem Research, Prospecting, and Economic Policies. If that popped up as a tooltip over each slider, that would seem to help a new player who is trying to remember what these councils all do.