This is caused by global illumination being calculated slightly differently for each frame. The GI is calculated as a pre-pass for each frame. Different views can cause slightly different results, and there's also a random element which can make subsequent renders different even if the view doesn't change.
To solve this you need to create a GI cache file (s), and have each frame read the same cache file(s). The best solution depends on whether you have Terragen 3 Professional or Terragen 3 Creative.
Terragen 3 Professional (using spherical camera mode):
1) Set the camera projection mode to Spherical, with rotation 0,0,0.
2) In GI settings, tell it to write to a GI cache file.
3) Render an image, so that a GI cache file is generated.
4) In GI settings, tell it to read the GI cache file you previously generated.
5) Render your skybox images.
Terragen 3 Creative (does not have spherical camera mode):
1) In GI settings, tell it to write to a GI cache file, including "%04d" somewhere in the filename (not including quotes).
2) Render your 6 skybox images. Each frame will generate a GI cache file to disk, instead of rendering a final image. It should generate 6 files.
3) In GI settings, tell it to read one of GI cache file you previously generated (and one in the sequence will do). Set the blend mode to "Equal Blend Within Range" and set the "number of files to read" to 6. The idea is to make sure that whatever you render from now on, it will read all 6 caches and combine the result.
4) Render your skybox images.
For more info:
http://planetside.co.uk/wiki/index.php?title=Terragen_3_Global_IlluminationMatt
