I had the same problem. You generally have to fiddle with whatever resolution settings you can through the game options, eqconfig.ini file, shortcut properties, and in game menu (once you can get to it).
It's kind of a pain in the ass but you'll eventually get it just right. I suggest running the game in forced 640x480 resolution with XP compatability turned on (if running vista) and then changing the resolution to your native resolution in the eqconfig.ini file within the folder. That's the only way I could reliably set my resolution with a 1366x768 widescreen and vista.
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