Just a quick one: Today I was trying to replace a preference file that we install via a package with a profile. It just didn’t work. Restore the plist file and it worked fine. This mystified me, and initially I thought I was just doing something wrong. And then I had an inkling of what could be happening.
I tossed the binary for the software-in-question into the Hopper dissambler and started searching for references to CFPreferences and to the path for the plist file. Sure enough, I was able to follow through the code and determine that the software created a proper plist, but that it was manually creating and reading that plist file; it didn’t use the preferences system to get its preferences.