Microsoft Word can do some particularly frustrating things with formatting....suddenly, one piece of an ordered list will be bolded, and you aren't sure why! Or something you want indented is refusing to indent...
I can't guarantee it will fix all your formatting problems, but there is a handy way to see what's going on.
From the "Format" menu, choose "Reveal Formatting".
A right-hand frame will appear. When you highlight any text, the formatting of that text will be displayed in the frame. You can click on any of the underlined formatting categories (like "Font" or "Alignment") and adjust the setting for the highlighted text.