The problem with any bench marking is that FF14 is poorly written and poorly optimized, and therefore has issues where others do not. So the typical stuff:
Make sure you have latest drivers and profiles for the game, yada yada and do a clean install of your video drivers.
Disable Crossfire if you have it, see if that helps (Crossfire especially seems to have issues with this game, more so in windowed mode if I understand it correctly.)
Possible I suppose that there are corrupted game files. Go to your Documents / My Games / Final Fantasy XIV / delete everything. Run the configuration program and set all of your graphics options etc. again (this will re-create the necessary files).
Uhm... Is your GPU or your processor or overclocked? If so, turn off any over clocking. I can give you the technical reasons why this is a good idea in general, and why its a great idea in particular for FF14 if you like, but the short version is 14 creates instabilities in OC'd systems that won't appear in other programs because 14 is poorly written.
Lets see... May sure you don't have any other Direct X programs running - its probably not that (because you aren't getting a direct-x error) but there are some DX capable programs that cause memory/driver issues with 14 (for example, Adobe Flash, the current version of which is extremely buggy to begin with and causes issues with 14).
Try it all without borderless window scripts and dual-box windowers if you use them (Evo, etc.)

See if that helps.