I discovered that MetroWerks’ standard libraries don’t understand Unix-style paths in CFM projects. When I call fopen("/Library/Preferences/com.absolute.settings","w+b") it creates a file called /Library/Preferences/com.absolute.settings in the current directory. When I converted my project to Mach-O, it worked correctly.
I should probably be using CFPreferences to get the proper path, although my settings file isn’t a standard XML preferences file.