Not a problem with the Mods or the Refueling Op you are running.
Changes were made to the Dynamic movement of the Kerbol star in 1.3 it is now meant to be choppy to fix some shadow issues, please see the below link and the associated bug tracker ID 15298 (pre-release)
http://forum.kerbalspaceprogram.com/index.php?/topic/161388-suns-dynamic-lighting-issue-in-space-center/
Edit: A dev post has been written regarding the lighting/shadows change here:
http://forum.kerbalspaceprogram.com/index.php?/developerarticles.html/enter-the-shadows-r205/
According to the above post, it seems this is an intentional change, though in my opinion a bad one, the transition of the sun is way worse than flickering shadows were since the shadows now update incrementally and the lighting globally is now noticeably worse, but I suppose this closes this topic, and I'm only a little annoyed that this was changed and not well documented in the patch notes since that would have saved me my troubleshooting time
Mods can close/delete or whatever this thread, I'll likely not monitor it further (Edit: this post is now linked to by other similar issue posts, please do not remove)
Thanks
Edit: A dev post has been written regarding these changes:
http://forum.kerbalspaceprogram.com/index.php?/developerarticles.html/enter-the-shadows-r205/
