He's not the only one. I have a fresh install of Unity, fresh install of NGUI, and a fresh Scene and the exact same problem happens to me.
Whenever I try to create a font with Font Maker, I click create the font and it opens the atlas changed dialogue. i click ok, get a spinning wheel for a second, and unity crashes. This happens EVERY time.
However, if I create the same font WITHOUT selecting an atlas, it works fine, every time.
I can then select that font and the atlas I want, and "replace the font", and it *seems* to add it to the proper atlas without any fuss.