Problem one: the URL for all my posts is saved as Permalink: http:// my domain .com/wp-content/uploads/2014/12/ with the file name at the end.
Problem 2: The footer menu disappears all by itself on random pages - no rhyme or apparent reason.
Your help would be greatly appreciated.
Unfortunately, I think this sounds more like a corrupt WordPress installation. The wp-content/uploads folder is where your media is stored. No permalink should have this type of URL structure - ever.
It could be something as simple as an unclosed tag within your content. If you can post a link to your site, I may be able to be of more help.