I'm getting exactly the same issue - SCOM 2012 R2 server with Exchange Server 2013 MP (15.0.665.19).  Windows monitoring works fine on the Exchange servers and the agent is in a healthy state.  I receive monitoring information for everything except for Server Components > Exchange IIS Application Pool and Server Components  Mailbox Database Copy.  The monitors are both enabled by default.  Does anyone have a resolution for this?  Thanks in advance...