Hi NZ, someone requested the ability to save the chat window size/loc at the character login. The feature was rolled out before properly tested it and results in the in game window losing its settings and returning to default. I believe they have fixed the bug in the base line source code.
What you can do right now to fix the problem on your end is ...
Edit your MQ2ChatWnd.ini file :
[settings]
NoCharSelect=on
You may also like to remove the news window by editing your MacroQuest.ini file :
[MacroQuest]
CreateMQ2NewsWindow=0
Hope this helps you out.