Thanks for contacting WPML forums support. I'll be glad to help you today.
1) It seems you use the same menu as a Primary and Footer menu, so you need to create a different menu and assign it as a Footer menu.
I don't think this relates to WPML because you haven't translated your menus yet.
2) Could you please share your Debug information with me?
You can read a detailed explanation about it here. (http://wpml.org/faq/provide-debug-information-faster-support)
The debug info will give me much information about how your site is configured.