I am not sure whether or not this is supposed to happen. I usually keep my chat windows in the corners of the game window, but every time I log off, they return back to their default position. I have tried Alt+O and loading layouts, but they take me to layouts that I had a long time ago and are now obsolete. That just results in me having to reposition everything all over again! It's strange because in the Load Layout window I get to see all my saved past layouts, but the layout I just made is never saved. How come it doesn't save? I don't want to keep readjusting my UI every time I play.
What method are you using to log off? Using /camp is your best bet. Using /exit or /quit doesn't always save settings.
I use Ctrl+x, although I occasionally do use /exit once in a while. Maybe I might have put in the wrong one this time. I'll try using just camp and see what happens.
Are any of your .ini files write protected / does the user you are logging into have write access to that file? Using /camp will try to write out your settings when you've logged out.