I am managing 20 or so Apple computers running 10.6.4 with a Mac Mini Snow Leopard Server (also 10.6.4). I am using the built-in OpenDirectory in addition to Kerberos to bind the clients to the server. Users have networked homefolders (stored on the server) that they can access by logging into any of the computers (much like a lab environment). Using the Workgroup Manager utility I have been applying Managed Preferences to the machines. Many of the preferences work, I can get the dock on the left, auto-create the logged in user's iChat account and auth via Kerberos, etc. However, it has been increasingly apparent that many of the settings just do not work. None of the settings under Media Access not work at all, though mcxquery shows them as being enabled. Additionally, Bluetooth disabling, auto-importing iCal accounts, and providing a predefined set of Safari bookmarks all do not take effect even though, as before, mcxquery shows what I would expect to see with the settings enabled. I've stumbled over a number of forum posts with problems similar to what I am experiencing, all without resolution. Any insight is appreciated.
If this is at a school, give Apple support a call. They offer free support to public schools in the US at 800-800-2775. When asked for the product that you're calling about, say "XServe" or "Mac OS X Server" to get to the department that you want.
I don't know if you're still trying to solve this or not, but a thought just hit me.
Some MCX settings can be overridden. For example, if you turn something on at the workgroup level and turn it off at the computer or user level, it will then therefore be off.
Also, there is a "guest computer account" which can have settings applied to it. Any computers not specifically listed under the "Computers" tab will have these settings instead.
I don't think that these issues are happening in your case, as you have the data in mcxquery telling you that the MCX settings are active. However, pointing this out may help you make some connection that neither of us made before now.