Symptoms
Assume that you use transaction replication that the Distributor is an instance of Microsoft SQL Server 2012 or SQL Server 2014. The publication of the transactional replication contains any combination of articles that is made up of views, stored procedures, table-valued functions, or scalar functions, and the Copy Permissions article attribute is true. When you apply the snapshot to a new Subscriber, the explicit permissions (GRANT, DENY, REVOKE) on the published articles cannot be replicated to the Subscriber. These permissions are not present in the ".sch" file that is created in the snapshot folder.
Resolution
The issue was first fixed in the following cumulative update of SQL Server.
Cumulative Update 4 for SQL Server 2014 /en-us/help/2999197
Cumulative Update 1 for SQL Server 2012 SP2 /en-us/help/2976982
About cumulative updates for SQL Server
Each new cumulative update for SQL Server contains all the hotfixes and all the security fixes that were included with the previous cumulative update. Check out the latest cumulative updates for SQL Server:
Status
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.