The Reader XI settings seem to be (like so many other Adobe products) ridiculous. What you need to do is set the preferences for update and EULA, etc, as some user (whoever), and either use FEU and FUT if you're making a .dmg package.
If you're like me and make .pkg installers, then write a post-flight that copies the com.adobe.Reader.plist file that's created to all existing users' /Library/Preferences and System Template Library/Preferences so new users get the settings from the start. I put it someplace central in the package, like in /Library/Preferences then copy that out to each home folder (~/Library/Preferences).
