Paragraph style problem

I don't know. At 544 pages, you should be leaning heavily on strict use of paragraph styles for the overall paragraph and character styles for the bits of italic and bold, etc. Maybe you are practicing the use of styles and the document only recently starting exhibiting this strange behavior. You could try this:

1. Examine any paragraph styles and make sure none are based on "Basic Paragraph Style". If so, a mere copy'n'paste may have triggered a change to the basic paragraph style, and this trickled down through some of your paragraph styles. It is better to make your paragraph styles based on "No paragraph style".  
2. Export your publication document out to .IDML and then re-open the .IDML file to restore an uncorrupted .INDD file and see whether the problem goes away.

If it is not an applied Character Style, then does the paragraph style show a + sign next to it? It might simply be "overrides". You can remove overrides by either Opt/Alt clicking the paragraph stylename or clicking the button at the bottom of the Paragraph Styles panel which is labeled "Clear Overrides in Selection".

Check the Character Style panel: do you have a character style selected? Usually, when you inspect the Character panel, the panel should be set on None in order for the paragraph style to not be overridden.