Hm... maybe you make a misinterpretation of the multiple menu setup. Different menus like you created are for situations where each menu has its own pages. So a page can only be part of 1 menu tree. In your case the top menu and main menu should have different pages. If you want to show the same (sub section of) pages but in 2 different places and probably different layouts, then use 1 menu but different commands and/or different CSS.
Please look here for a good explanantion of menu setups, and especially the part about "Difference of multiple menus and multiple menu calls":
http://www.websitebaker2.org/en/help/designer-guide/multiple-menus.php