The problem went away after I disabled anti-aliasing and anisotropic filtering in the SkyrimPrefs.ini. This is what I set:
iMultiSample=0
iMaxAnisotropy=0
I tested for 10 hours with no issues whereas before I'd see the glitch roughly once an hour.
I found the suggestions here:
https://www.reddit.com/r/skyrimmods/comments/3bt5nm/help_polygons_of_various_colors_are_everywhere/
https://forum.step-project.com/topic/4084-crazy-flickering-and-polygons/?do=findComment&comment=65449
They say this needs to be done when using ENB, but I'm using ENBoost without ENB effects. My guess is that either Skyrim or my graphics card has difficulty doing anti-aliasing or anisotropic filtering for objects that are already fairly detailed. My graphics card is far under its limits when this happens, so it could also be a driver issue.
Anyway, this is solved. Hope it helps someone else :)
