Hm, strange - I did a quick test with 2 button lists in a menu screen and that worked fine.
Generally, only one of the GUI boxes is active at a time (i.e. has the focus) and reacts to menu input (accept, cancel, horizontal/vertical). Clicking on the other GUI box should change the focus to it and allow menu input. Depending on the choice settings of the GUI box, a click on a button/choice can also directly use it.