Concerning the map, have you made sure that the image is flattened? I'm not familiar with the program that you are using, but under the layer menu or either by right clicking on the single layer, there should be an option to flatten the image. Also make sure alpha channel is off and that all pixels are locked--there can't be any transparent parts on your map.
As for the markings, are you able to see the marking names in the character creator at all? If not, you may have the markings.cfg in the wrong place. Make sure that the .cfg is pasted directly into the main Feral Heart Folder.