I found some things strange in my last hybrid Intune project.
The Customer has a new SCCM site – installed with SCCM 2012 R2 Sp1 and upgraded to CU1.
The email profile are not ot be found in the SCCM console:
Screen shot from a SCCM R2 SP1 CU1 installation where the Microsoft Intune Subscriptions was enable before SP1 upgrade
Screen shot from a SCCM R2 SP1 CU1 installation with the Microsoft Intune Subscriptions.
The folder with Company Ressource Access are missing.
After trying different workarounds without luck – i looked and the SP1 was missing.
Downloaded the 6 MB ISO – installed it and every things Works.
Now I can create a Email profile.
Cloud First 
Hello Sir-
Can you please clarify when you state: “Downloaded the 6 MB ISO – installed it and every things Works.” where you downloaded this ISO from?
I am running into this exact same issue and could use some guidance.
Thank you,
-Jared
You can download SP2 from here https://www.microsoft.com/en-us/evalcenter/evaluate-system-center-2012-configuration-manager-and-endpoint-protection
Hello Jared – there is also released a hotfix yestoday https://support.microsoft.com/en-us/kb/3106034