I'm the author - Charity Navigator isn't very useful because it doesn't tell you whether the program delivered by the charity actually helps people, which is by far the most important and most frequently lacking factor. The only thing CN is useful for is identifying outright frauds, and even then it's not amazing.
As you can see GiveWell has investigated AMF including its finances in vastly more detail over 4 years than Charity Navigator has ever investigated anyone: http://www.givewell.org/charities/against-malaria-foundation