Looks like you've made a change to the x.position of the navigation menu items, and then the setting screen with default positioning is overlapping when it is displayed.
Did you change the gui.navigation_xpos parameter in gui.rpy to align the list of menu items with your background image perhaps?
If you want to see more about how it is put together, you can see how the main menu and sub menus are setup in the "screen nagivation:", "screen game_menu" and similar parts of the screens.rpy file
Some things you could try:
1. find the "screen game_menu" which provides the structure for all the sub-menus and adjust it to take the moved navigation menu items into account. You would also have to then modify all the navigation sub-screens such as "preferences" etc. to match the new available width.
2. modify the game_menu screen to hide the navigation menu while the sub-screen is open (hint: comment out the "use navigation" line and try if that works)
3. change your navigation menu position back to the default position, even if that means modifying your main menu background image