It sounds like your deployment environment is running .NET 3.5 but you are deploying a build for .NET 4. You need to change your deployment environment to use a .NET 4 application pool to make it use .NET 4 runtime.
The error happens because of a difference between .NET 3.5 and .NET 4.
In .NET 3.5 some sections need to be declared in Web.config, but in .NET 4, the same sections are declared in machine.config so they are not needed in Web.config. So you get this error about an unknown section because it is not declared in web.config and it means you must not really be running under .NET 4 or you would not get this error.
Hope it helps,