First off this goes in the Game Help section not presets and markings since this area is to share markings & presets not ask for help with them ^_^
But yeah usually when this problem happens it has to do with the markings.cfg file. If the coding isn't wrong some how were you sure to close and restart the game if you downloaded while the game windows was open? Also since I'm not sure which markings you're talking about can you link me? It will help me help you better