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.I can't see if alpha channel is on or off (I actually looked recently and didn't find anything about it), and there are no transparent pixels.
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.
You can use GIMP simply for the saving part.
Here's a tutorial that includes some steps for making a height-map: https://feral-heart.com/smf/index.php?topic=62143.0
You can also try using & modifying (copy and paste your heightmap into it) this:
http://www.mediafire.com/view/ausqlcih5y3qd3v/TestHeightmap.jpg
It's just a flat, standard heightmap for getting started... it has everything set up already.
You'll have to put it somewhere fh can find it though.
Also: You can change the .jpg to .png by using "file > save as" if you want to keep using .png, which makes the map smoother. =)