After a normal installation without any updates, does a win server 2008 R2 with SP1 including the .net framework 3.5 or 3.5 with sp1+?
You'll need to "enable" it (install it) using the Add Features function in Server 2008 R2. It is not enabled by default but it already has the installer.
In the Server Manager console, click Features to see if it is listed in the right-hand pane. If this is a fresh/clean install, it should not be already listed.
Click Add Features, expand .NET Framework 3.5.1 Features, click the checkbox next to .NET Framework 3.5.1 and click Next.
A few other required services and features will be listed that need to be installed as part of this framework, but you should just be able to continue through the wizard and when it completes you'll have .NET Framework 3.5.1 installed on the system.