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Consider the following scenario:
In this scenario, the enroll.exe utility does not read the user name and password in the enroll.cfg file and you are prompted to enter a user name and password manually. Therefore, the certificate is not installed automatically.
For a hotfix to resolve this issue see our latest Configuration Manager KB article below:
KB978914 - The enroll.exe utility for Windows CE 5.0 mobile devices does not read the user name and password you entered in the enroll.cfg file that is used for authentication
J.C. Hornbeck | System Center Knowledge Engineer