I see why you have the problem, you don't open the 2D display that is showing the Checklist. I always open the 2D display that I use to view Checklist in, so pressing the ALT + Arrows, doesn't move my view around, nor open the P3D menu.

To be honest, I have never really thought about using the checklist without opening the 2D display panel, as the display showing the Checklist moves to each view I go to (i.e. it stay visible each time I press the A, Shift + A, S, or Shift + S), so I find it much easier to check everything on the Checklist, while it's  visible as I'm doing it.