I was getting the error below when trying to deploy to my SQL 2008 R2 cluster, which was odd since I had never had any trouble before. The problem ended up being that when I double clicked on the SSISDeploymentManifest file my computer was using the SQL 2012 version of the deployment utility because I had recently installed it. Once I used the 2008 utility everything worked fine.
Exception details: Microsoft.SqlServer.Dts.Runtime.DtsRuntimeException: Storing or modifying packages in SQL Server requires the SSIS runtime and database to be the same version. Storing packages in earlier versions is not supported.
---> System.Runtime.InteropServices.COMException: Storing or modifying packages in SQL Server requires the SSIS runtime and database to be the same version. Storing packages in earlier versions is not supported.