Unless JustSomeDude released a new version, EQW doesn't work with the latest patch yet. I checked the website Friday I think and it was still at version 2.41 and he was MIA from the forums.
EQW is EQWindows and allows EQ to be run in windowed mode. It was developed prior to the time that Sony changed EQ to allow the game to be run in windowed mode. In my opinion, EQW still does it better. :P It also has a checkbox which you can uncheck to skip the patcher. The EQW website is
http://www.eqwindows.com