Solved! It seems we did not try enough alternate themes to the Cool Gray theme. The Vibrant theme fixed all the major problems, but still has some minor issues, such as Italic text on WD not present in FileMaker, and the need for a black background with white text for one of the portals. Other than that, functionality is 100%!
Don, you may mark your "Solved!" comment as correct answer, so others may find it quickly if they have the same problem.
WD and themes can be an issue and I'm glad you found a theme that works!
If you are using WebDirect, I would highly recommend upgrading to FMS16. There have been many improvements and bug fixes since V13.