I had EXACTLY the same problem.
What you need to do is go into your eqclient.ini file which can be found in your EQ folder. You need to find the 'WindowedWidth' and 'WindowedHeight' and manually change them to whatever resolution you are using. Save it and you are good to go.
Make sure you do it when you haven't got EQ open, otherwise it won't work =p
Hope this helps!
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