Make sure that you have updated your Company Portal app to Version 4.0.14264.0 when using Intune with System Center 2012 Configuration Manager R2. It was released at 18.10.2013 and you will find it here:
http://www.microsoft.com/en-us/download/details.aspx?id=36060
For signing the app refer to this blog post:
http://blog.hosebei.ch/2013/06/19/sccm-2012-sp1-windows-phone-8-portal-app-and-azure-active-directory-allowed-characters/
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