If you are using a single computer configuration for BizTalk 2006 R2 and if you are experiencing performance degradation, there is a simple setting that you can try before spending too much time attacking performance issues.
Disable SQL Server Shared Memory Protocol
1. In SQL Server Configuration Manager, expand SQL Server 2005 Network Configuration, and select Protocols for MSSQLSERVER.
2. Right-click Shared Memory, and then click Disable.
3. Close and Re-cycle SQL Server.
If you are using SQL 2000, disable Shared Memory using SQL Server Client Network Utility.
Again, this issue may not occur on a multi-computer configuration (database server is different from the BizTalk Sever).