I'm using DX9 (I get horrible framerates in DX11), and here is the hotfix I used to solve the problem:
-Open up FFXIV.cfg (MAKE AN EMERGENCY BACKUP COPY IN CASE YOU MESS UP!!!)
-Scroll down a bit, look under Display Settings
-Check the values for ScreenTop and ScreenLeft
-If either of these two numbers are not 0, change them to such.
-Save the file, reload launcher
Once you do this, it should stay. I haven't had to fix mine since making that edit, and the game loads as it should.