Checked your file ... and confirmed, the sphere has the same size as the planet.
Your file:
<sphere
name = "Sphere 01"
gui_use_node_pos = "1"
gui_node_pos = "0 0 0"
gui_group = "Objects"
enable = "1"
show_b-box_in_preview = "1"
visible_to_camera = "1"
visible_to_other_rays = "1"
cast_shadows = "0"
centre = "0 -6.378e+006 0"
radius = "6.378e+006"
... until I changed the radius myself, saved the file, restarted terragen, opened the file and everything is fine.
My XML has this to say:
<sphere
name = "Sphere 01"
gui_use_node_pos = "1"
gui_node_pos = "0 0 0"
gui_group = "Objects"
enable = "1"
show_b-box_in_preview = "1"
visible_to_camera = "1"
visible_to_other_rays = "1"
cast_shadows = "0"
centre = "0 -6378000 0"
radius = "6378001"
So it might be an issue of the current Beta-Release. Somebody with the current version has to check it, too.
Volker