We updated the Pilcrow theme recently which may have led to the changes in the Featured Image that you described. We've fixed a bug related to that and sounds like you were able to get everything back to how you'd like it. If you have any continuing issues with the featured images and Pilcrow, please do let me know (replying to this thread is great).
Regarding the mobile menu, WordPress.com will default to listing all of your pages in the menu if the Primary Navigation option isn't selected in Pilcrow.
To resolve this, you can visit the Menus link in your dashboard at Appearance->Menu. Give your menu a name, then select which pages you'd like in the menu. Then, click "Create Menu" in the upper right.
Lastly, after saving it, a new "Manage Locations" tab will appear near the top. Please click on it and ensure that your new menu is selected for the Primary Navigation.
More instructions, along with a screencast, can be found at http://en.support.wordpress.com/menus/
Please let us know if you have any questions or if there is anything else we can do for you.