This was a bug last month and one of the devs said to try this work around (but then again they also said it was fixed internally)
As a workaround, if you switch to restored windowed mode, open or toggle a UI window, and switch back to maximized windowed mode, then it will update the settings so as not to open the copy layout window next time. This can be done by:
- Launch game client
- Login a character
- Click the restore window button in the title bar
- Press ALT+F to open the Friends window
- Click the maximize window button in the title bar
The character's UI .ini file should be updated sufficiently for the copy layout check.