Consider the following scenario:
•You install the following update on a computer that is running Microsoft BizTalk Server 2009:
◦Cumulative update package 6 for BizTalk Server 2009
•You add resources or import MSI files to deploy the BizTalk Server 2009 applications that include the following BizTalk Server 2009 assemblies in BizTalk Server 2009 Administration Console:
In this scenario, you cannot deploy the BizTalk Server 2009 applications. Additionally, you receive the following error message:
Error saving map. Stored procedure returned non-zero result. Check if source and target schemas are present.
The issue only happens when the map's .NET namespace is a subset of the schema's .NET namespace. The logic we used to figure out if the schema’s .NET Namespace is a part of the map’s .NET Namespace, we assume the map's .NET namespace is a subset of the schema's .NET namespace. This issue occurs because BizTalk tries to deploy the MAPPER_ASSEMBLY assembly before the SCHEMA_ASSEMBLY assembly. However, the MAPPER_ASSEMBLY assembly uses schemas in the SCHEMA_ASSEMBLY assembly.
Microsoft has confirmed this is a problem in BizTalk Server 2009 CU6.
If you need the solution of this problem, please contact Microsoft Support: http://support.microsoft.com/contactus/ .