try deleting server/charactor ini files. Sometimes they get corrupted and give problems with window settings. They should recreate themself when you log in again ( you will have to re arrange your UI though.
another thing that causes this is when something is updating in the background and giving a pop up ( like an AVG update notice, or stuff like that) or when a program has been set to always be on top, this will make that happen. Like VLC set to always be on top while eq runs only works in windowed.
Also if you switch between both full screen and windowed alot the ini can get messed up/confused as to what setting you are on. It can sometimes rewrite the ini file slower than some switch between the setting.
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