It sounds like this is a problem with your yourserver_charname_eq2_uisettings.ini file.
Try making a new character and see if the affected windows position correctly. If they do then it is a problem with the xxx_xxx_eq2_uisettings.ini for your specific characters. You'll need to delete/rename the file so the game can generate a new one. Doing this you'll have to reposition all your windows again.
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