I've had this problem for years and I almost always run into it in a lengthy play-through, yet I still don't know what causes it, but I can assure you, it's not your graphics card or your INI settings or your sky texture.
I currently have two subsequent saves, one with the stuttering night sky and one without. There's absolutely no change in any settings between them, the timescale value is the same and absolutely no change in mods either. I just finished my business in Torvald's Cave and then went to Mzulft. I noticed the problem when I got out of Mzulft but then I realized the problem had already started as soon as I entered the place. There's about 10 minutes between these two saves and sometime in between Torvald's Cave and Mzulft entrance the stuttering started. I'm not saying that these two places have something to do with the problem, but it's very likely a bug caused by the game itself. Could also be a bugged script (either a vanilla script or from a mod) or too many of them, or a script or some FX attached to something it wasn't supposed to. Whatever it is, it's a bug.
Edited by Kinlar, 31 October 2015 - 04:25 AM.