I'm having more or less the exact same problem. I just finished building a new computer last week after coming from a laptop and this issue has followed me to my new computer. The only thing at this point that could be affecting my game is that (even though I started new games completely vanilla), my save games followed me with Steam cloud. I have since disabled the steam cloud, deleted all my saves and totally removed any traces of the game from my computer. Now in the process of re installing skyrim, I will update when its done with photos if the problem persists.
Im also about positive this is not a driver or faulty hardware issue either as this computer plays other games flawlessly.
specs: GIGABYTE GA-Z87X-UD5H
i7 4770k
evga gtx 770 sc 4g