This took me a while to figure that out but, but it is logical that the Configuration Manager client runs in a different context since the client needs unlimited access to the system. The Tilde (~) means current user so when checking and changing “ ~/Library/Preferences/” you will actually check and change the file located in /users/root/Library/Preferences/. So for this reason you see that nothing is changed when pointing to a preference file in a Configuration Item in Configuration Manager like this ~/Library/Preferences/. System preferences can still be changed via the native Mac OS X preferences. The context in which the Configuration Manager client runs and now changes preferences or running scripts is not the current user but the ROOT user. In an earlier blog I described how you could use the $USER variable if you want to change a user setting, but for some reason how the Configuration Manager clients interacts with Mac OS X is changed. One of the things I showed was the ability to change user preferences in Mac OS X.
Mac OS X support by Configuration Manager 2012 R2 has two ways of supporting Settings Management namely, managing settings through preferences directly or managing it through Shell Scripts. Today I presented a session about Mastering Apple OS X with Configuration Manager 2012 R2 at the Swiss Configuration Manager User Group in Bern.