I noticed today that some data sources where being missed using the schemas listed in the data sources.

If you are using Sharepoint 2010 with SSRS then you will want to update the queries that contain:

http://schemas.microsoft.com/sqlserver/reporting/2005/01/reportdefinition or

http://schemas.microsoft.com/sqlserver/reporting/2008/01/reportdefinition

http://schemas.microsoft.com/sqlserver/reporting/2010/01/reportdefinition

The new schema worked on both 2008 and 2012 reports. I am not sure if this is a Sharepoint Issue, but if you are seeing missing connections, then you will want to update the query accordingly.

These reports will NOT reflect Sharepoint Permissions, and those are not stored in the ReportServer.