Hi satyra,
I am also experiencing this issue. I just updated to Word Press version 3.6, and updated the theme to a newer version as well. I have the menu order correct on the web, but it's reverse on the iPhone/mobile, where what shows in the navigation is not the same as the Home Page on the screen. Users have commented that they can't get to the page they want and I've instructed them to take a couple of extra steps where they click to another page in the navigation and then back to the original page they had wanted to view.
I read some threads regarding this and it seems the resolution is for an update to come out? If there are any other ways to fix this problem in the meantime, let me know and I can incorporate them.
Thanks for your continued help!