WMF is the Windows Media Format Runtime. All Front End Servers and Standard Edition servers where conferencing will be deployed must have the Windows Media Format Runtime installed. WMF is required to run the Windows Media Audio (.wma) files that the Call Park, Announcement, and Response Group applications play for announcements and music.
The issue here is that the WMF package version has changed for Windows Server 2008 R2 SP1. The workaround is to run the following command from an elevated CMD prompt, as shown:
%systemroot%\system32\dism.exe /online /add-package /packagepath:%windir%\servicing\Packages\Microsoft-Windows-Media-Format-Package~31bf3856ad364e35~amd64~~6.1.7601.17514.mum /ignorecheck
Once the package is updated, restart the computer when prompted, and continue with the installation. The Lync setup check will detect that the a proper version is installed and will proceed.