I am using a Radeon 5800 card and have been having some visual disturbances in game also. They are fairly subtle and I have only noticed them over the past few weeks. Most noticeable is on the ferry the water no longer looks beautiful, but blocky and a bit foggy. Otherwise I have an intermittently noticeable horizontal bar about 1 inch thick and it rolls down the screen from top to bottom, causing the area in question to become "warbly" or blurred.
I downloaded the latest graphics drivers, and have not noticed it using any other application on my pc other than ffxiv. I am not sure if it is game related, or a problem with my hardware/software. The pc is less than 6 months old though, so hope its not the graphics card going out already :P. Any Ideas?