Can you give me an example that seems out of place?
Edit:
Doublechecked the system and it is working correctly.
Without more information about the exact issue, I have to guess here, and what I think is most likely happening is a difference in functionality vs expectation.
AutoMenu doesn't set choices, it chooses them. You have to play through (or fast forward through) a scene where the choice happens for it to have an effect on the game. If you skip over it, or past it (with Scene selector or Day selector), then AutoMenu won't choose any options. For example, the first option to set birth control for Summer happens in the first scene for Day 11. If you start in Day 11 scene 2 (or latter), then the choice menu didn't play, AutoMenu didn't make any choices, and the system uses the default value (birth control off).
If you are playing the game out of order (jumping to scenes), then you'll have to use the Do Over menu to properly set any past choices (including birth control).
If you are playing the game in a liner order, not skipping over scenes, and still encountering this issue, let me know where you found it. It is most likely either a bug, or a dialogue line that is just out of place.