There is a subtle regression in the configuration parsing between 2.0.6 and subsequent versions tested (2.0.7, 2.0.8, and 2.4.0-rc2).

If you quote your keyFile parameter in a mongodb.conf this works fine in 2.0.6:

keyFile="/etc/mongodb/keyfile"

In 2.0.7 and later versions tested, the identical config produces an error suggesting the keyfile does not exist:

error getting file "/etc/mongodb/keyfile": No such file or directory

The solution is to remove the double quotes:

keyFile=/etc/mongodb/keyfile