When applying the changes historically it would only reset the default value for those who had not picked a preference manually so as not to override any invidual choices (eg. turning on email for those who had opted out). The number it provides should tell you how many users it affected, which would be only those elligible and not necessarily the total amount of users.
You should be able to set the values using the rails console for those user preferences. 
There should be some tips in this topic Edit a user preference for everyone or a subset of users