So I reinstalled Skyrim after months of break, and found new problems I have never encountered before.

The smoke effect on the loading screens might flicker purple (EDIT: sometimes it's blue), while some textures in-game might flicker red.\

Screenshot: http://i61.tinypic.com/xrql3.jpg

At first I thought it might be mods or Mod Organizer (first time using it), then I disabled all mods and tuned down the graphical setting to the lowest, problem persists.

Anyone knows why this is happening?

Did you update your video card drivers before you started playing again?

Yes

This seems to have been a somewhat frequent problem with the most current AMD drivers, though some people have reported problems with the latest Nvidia driver as well. You might try rolling your driver back to an earlier version and see if this fixes your problem.