This happens because the xml-files in [Assets/XML/Art] does not have the correct path to the graphics-files they are trying to define. The graphics-files should be in [Assets/Art].
For the two leaders: The file
CIV4ArtDefines_Leaderhead.xml is the one you need to check. There is a field called <Button> that contains the path to the files needed in this screenshot. Change those so that they point to the file in the [Assets/Art....] folder.
For the flag: Check the file
CIV4ArtDefines_Civilization.xml. The <Button> and <Path> entries should be checked.
Make sure to save in the XML format, not in TXT format. You can do the changes in Notepad, but I recommend Notepad++ (notepad will always try to save as txt, unless told otherwise, without even telling you).
Oh, and make sure to check for spelling errors. I have done a bit of this myself. Just ONE TINY spelling-error (like two l's instead of one) can take hours to fix if you don't know where to look.
I hope you figure it out. Happy Civ'ing.