Yes, change the menu color if it really bothers you. Which place are you referring to when you said a room with boxes? Pressing some button (I think it was Select, but I'm not sure) will give you the directions, so you'll know where you are and where the exits are. If that's the inn in Sector 7 slums, it usually helps when you go to the bar. If that doesn't help you, it might be that your party is about to invade the next Mako Reactor. In that case, head to the Train Station. I can't remember the exact details since I haven't played the game for like 4 years.