When configuring "SEP Communication" in Advanced Threat Protection (ATP), checking the box to "Apply private cloud policies to all non-default SEPM groups" does not work. Some groups are still left without Private Cloud Settings. 

This issue occurs when pushing communication settings to 50 or more groups. 

This issue is resolved in ATP 3.0.5 and later.  For more information on upgrading ATP, see Symantec™ Advanced Threat Protection 3.0.5 Upgrade Guide.