Grumpy_Mike: No, that is the pin you put an extra high voltage on if you want to programme the grey scale correction rom.
It turns out I had read 4K7 as "47k". I replaced all the FET resistors with 4.7k and now the brightness is good.
When I power it up or run any of the Processing examples individual rows are different colors, but not individual LED's. To reduce complexity I removed the other two 5940's and reduced the matrix to 4x4, figuring I'll scale it once I get the basics working. Any ideas?
Video of the issue: http://dl.dropbox.com/u/6253968/rows.mov