Hi! Normally the only thing that should skip the main menu is these lines at the top of script.rpy
#Skip the main menu
label main_menu:
return
In case you still have this problem, make sure to delete script.rpyc (the binary file) to be sure it's up to date. Sorry for the late response, I hope this can at least help someone. Don't hesitate if you have any more question.
Have a nice day!