When users are Lync enabled in a Lync Environment (no OCS 2007 or OCS 2007 R2), the user property PublicNetworkEnabled is set to true by default when enabling users.
PublicNetworkEnabled is where MessageStats gathers the information from to report if the user is Enabled for Public IM Connectivity in OCS 2007 and OCS 2007 R2. Because PublicNetworkEnabled is true by default in Lync, you will see an equal number of Users to Users Enabled for Public IM Connectivity in the reports.
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STATUS
Enhancement Request TF00249951 has been submitted to development for consideration in a future release of MessageStats.