That information is stored in your server_character_eq2_uisettings.ini file. Make sure you do something with the windows in question (ie click a hotbutton or something) to ensure that it's placement is saved in the file, and make sure that file isn't marked read-only.
If that doesn't work, I think one of the other featured authors (I forget which) has a program that'll let you look into that uisettings file and see what's going on with those windows.
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