You might need a SCOM update. Up until recently, the SCOM agent would still load PowerShell 2.0 on some versions of Windows even if PowerShell 4.0 was installed.
The update you need is SCOM 2012 R2 UR7 and SCOM 2012 SP1 UR10.
Here’s an extract from the UR release notes (my emphasis):
CLR load order change
The current behavior for agents is to choose a CLR version based on the operating system version. For Windows Server 2012 and newer, the .NET Framework 4.0 is loaded. For operating systems older than Windows Server 2012, the .NET Framework 2.0 family is loaded. On management servers, the .NET Framework 2.0 family is loaded. This essentially maps the .NET Framework version used to the version available out-of-box on the server. The problem with the current behavior is that even if the Management Pack author knows that .NET Framework 4.0 is present on the system, it cannot be used.
In the new behavior, the agent loads the .NET Framework 4.0 if it is available else it falls back to the .NET Framework 2.0.
I originally came across this on the following blog:
Which PowerShell version is my SCOM agent using (or why I love SCOM 2012 R2 Update Rollup 7)