Windows embedded OS provide a subset of the functionality normally available in the standard variants of the OS. These are generally supported with the following caveat:

Windows Embedded versions are customizable Windows OS, best suited for embedded or kiosk usage and may only have a small subset of the full operating system features. Support for Windows Embedded will need to be evaluated on a case-by-case basis.

To support Windows Embedded OSes, you must define the Universal Write Filters (UWF) that determine what an application is allowed to change in the OS, see http://blogs.technet.com/b/configmgrteam/archive/2012/07/20/how-to-manage-windows-embedded-write-filters-using-system-center-2012-configuration-manager.aspx for details on how to set these for Configuration Manager. The UWF fall into two categories: File Exceptions and Registry Exceptions. 

For Nomad, UWF should be defined for the following:

File Exceptions

C:\ProgramData\1E\Nomad

Registry Exceptions

HKEY_LOCAL_MACHINE\SOFTWARE\1E