I was trying to work out why I couldn't replace the default marker images (copied automatically to /wp-content/uploads/wpgeo/markers) with my own marker image.
It turns out the the code is searching in /wp-content/uploads/wpgeo rather than /wp-content/uploads/wpgeo/markers
(the code that makes this decision is includes/markers.php line 83 - function get_image_url(), which only checks if the file exists in the $this->wpgeo_upload_dir.
Maybe I've misread the instructions, however thought it'd be worth me pointing this out.
All the best,