I'm running a GTX 1060 and like you, I don't have any problems with any other game. It seems to be something in Intrigue that's causing it. If you look in the patch notes, Brad said he screwed around with the sizes of the maps, save the largest ones (said he didn't want to get killed). Maybe what he did there messed with the graphics of the biggest maps? I don't know.
In any event, visually, it's not that big of a deal for me. I am wondering though if it does have anything to do with the game freezing on me randomly for 20-30 seconds at a time.