The following article on Microsoft TechNet is a helpful guide to using the Configuration Manager 2007 Client on Windows Embedded Devices:
Prerequisites for Installing the Configuration Manager 2007 Client on Windows Embedded Devices
While this article has some useful information, it has caused some confusion for users of Windows Embedded Device Manager 2011. Specifically, the section of this article that describes how to set registry exceptions and file exceptions for devices that use File-Based Write Filters (FBWF) does not apply to devices that have the Device Manager 2011 client installed. Device Manager 2011 allows you to distribute software to write filter-enabled devices that have the Device Manager 2011 client installed by using advertisements and task sequences that manage the state of write filters on those devices.
Following the instructions at the link provided above when configuring a device that has the Device Manager 2011 Client installed will cause issues with managing that device using Device Manager 2011. For more information about write filter handling in Device Manager 2011, see the Write Filter Support section of the Device Manager 2011 Administration Guide at: http://technet.microsoft.com/en-us/library/gg749244.aspx
J.C. Hornbeck | System Center Knowledge Engineer
App-V Team blog: http://blogs.technet.com/appv/ AVIcode Team blog: http://blogs.technet.com/b/avicode ConfigMgr Support Team blog: http://blogs.technet.com/configurationmgr/ DPM Team blog: http://blogs.technet.com/dpm/ MED-V Team blog: http://blogs.technet.com/medv/ OOB Support Team blog: http://blogs.technet.com/oob/ Opalis Team blog: http://blogs.technet.com/opalis Orchestrator Support Team blog: http://blogs.technet.com/b/orchestrator/ OpsMgr Support Team blog: http://blogs.technet.com/operationsmgr/ SCMDM Support Team blog: http://blogs.technet.com/mdm/ SCVMM Team blog: http://blogs.technet.com/scvmm Server App-V Team blog: http://blogs.technet.com/b/serverappv Service Manager Team blog: http://blogs.technet.com/b/servicemanager System Center Essentials Team blog: http://blogs.technet.com/b/systemcenteressentials WSUS Support Team blog: http://blogs.technet.com/sus/