I am having exactly the same problem
In my case however it was the opposite: When I build the font the first time it looked corrupted (wrong UV offset). I wasted an hour after work trying to figure out what I was doing wrong - but I gave up.
Then this morning when I was booting up the project again it showed up all perfect.
But I was curious so I added some sprites to the sprite sheet and rebuild the atlas in NGUI - and voilĂ again - the font was broken. I restarted Unity - nothing changed, restarted again and again and eventually it showed up correctly again.
So there seems to be something broken in NGUI - not saving (marking prefabs as dirty) or not proper propagating changes to all related items (sprite sheet update affects fonts etc.). I would really really appreciate if this would be fixed sometime soon because upcoming projects will depend on NGUI and fonts working without issues.
I will post some screenshot the next time it looks broken again.