Hi @santsho!
The warnings about the static pages are also part of the upgrade process. The navigation menu feature by default is trying to change any static page it finds in your installation into a custom navigation menu item with the same path and the same content. If it already find one custom navigation menu item with the specified path, the upgrade process skips that static page from changing into a navigation menu item.
Now, regarding your issue, could you give more info? First of all, I suppose you where using both static pages plugin and also you had added corresponding custom navigation menu items(NMIs)? If so, can you confirm that after the upgrade, the NMIs have the same path and context as before? Another thing we can check is whether those NMIs are still at the previously assigned Navigation Menus. Those information could also be found at the Navigation Menus feature management pages.
Thanks.
@Dimitris_Efstathiou