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The problem you're having is because the Marker messages you are visualising in RVIZ are not related to the map within the map_server. You will need to translate the positions of the markers you currently have into map space and add them directly into the map as obstacles in order for them to be saved or for them to affect the path planning within the map.
RVIZ allows you to visualise many of the standard message types that ROS supports, what you see on it's GUI is not just a map but all the topics you've currently set it up to view. The map_server is just saving the map part, it has no visibility of any other messages being passed around ROS at the time, which includes your marker messages.
Hope this helps.
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