Aye aye!
Are you sure you replaced everything properly? You need to put the markings.png files in the textures folder for them to show up in the game. There will also be a CFG file in the MM3 folder named 'Markings'. You need to put that in the main FH folder and click replace for them to transfer the custom codes to the game.
This will connect the MM3 coding with the FH default coding so that you can see your/other people's markings.
Here is a very useful thread made by one of our members if you still can't figure things out. (:
http://www.feral-heart.com/index.php?option=com_jfusion&Itemid=2&jfile=index.php&topic=21635.0 (http://www.feral-heart.com/index.php?option=com_jfusion&Itemid=2&jfile=index.php&topic=21635.0)
Good luck in finding a solution!