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RVIZ markers specify their frame_id in the message, along with their pose. So if you specify a point at (0, 0, 0) then it will be shown at the origin of the given pose defined within the coordinate system of '<frame_id>'

I usually set the pose to identity to keep things simple, and calculate the marker points directly within the specified frame, but that isn't always appropriate.

Regarding the problem you describe can you post a screen-shot along with the code which produces it. We'll just be guessing without it.