I updated PCGen. It now includes the latest data files as well as the Magic of Eberron supplement. I also removed the data set that was screwing with armor.
To get Pc Gen to work better you should install the Core PCGen program first. You can download it here.
http://prdownloads.sourceforge.net/pcgen/pcgen581_win_install.exe
When you install it some variables get set in the resigtry that makes PCgen easier to work with. It will remeber which books you loaded last time you used it and you can get rid of those annoying pop up windows when you load the books.
After you install the Core PcGen program download the zip from my site and unzip it to the directory where you installed pcgen. Let it overwrite everything and you'll end up with the proper data files.
Is there any way I can get that file? I am playing in an Eberron game and would love to be able to use PCGen to make my character(s)!