OS X :: Emails Not Displaying Correctly?

I recently embarked on a quest to reorganize my font libraries and I think I messed something up! Capital A's with boxes around them show up in many of my emails (using Mail) instead of text, and the emails from my iPhone Notes don't load at all. I don't understand this because the MarkerFelt.ttc font is in the HardDrive-->Library-->Fonts folder.

Basically, I had organized my fonts within the HD-->Library-->Fonts and the Username-->Library-->Fonts folders with Font Agent Pro and moved them to a separate location so that I could manage them more directly. Everything was fine at first and then things started looking wacky in Mail. I moved everything back to its original font folders and it's still displaying incorrectly. I've attached screen shots of what I'm talking about so it makes more sense. I would really appreciate any advice on how to get things back to normal.