Not sure if this is related in any way as the fix but I closed the game then ran it as admin and it seems to have cleared up.

To clarify, it wasn't the restart that fixed it as I have fiddled with almost all the graphics options and restarted multiple times with no change.

edit: @Gospellus I am running teamspeak with the overlay enabled but it isn't hooking into FFXIV as far as I know.