So whenever I do shift+f1 and change the placements, or when I change the transparency of the chat box, the changes don't get saved after I re login/switch characters. This only happens to these two settings. Other settings are fine.
I don't think it's a problem in relation to clientconfiguration.xml... because I tried deleting the file all together. After I did that all the settings in the game were reset, and settings pop up during character selection like when you first installed the game, but the UI placements remain the way they were. (which was the way I have had, but not the default.)