Miaad,
Good catch and good question. I am most familiar with AP Style from my days as a journalist. And AP's rule is that you should, in general, avoid unnecessary capital letters -- which means, that unless they fit certain exceptions, the words should not capitalized. The exceptions are: proper nouns, proper names, popular names (i.e. "the Street" for Wall Street) and derivatives (derived from a proper noun and depend on that noun for meaning, i.e. American.) The reason I left some of them capitalized is that they seemed to be a part of an official title of an academic program -- Department of International Relations, as an example. Short of being able to converse with you I made a decision to leave them as you had originally written them, trusting your judgment. If I had to make a recommendation it would be to be consistent -- so go with the lower case in the examples you cite. Please let me know if this makes sense and happy to continue to collaborate.