Hi,John,
Which report did you look at for the audio quality?
There are many reports in Lync monitoring server,and not only one includes the audio quality,here are the description for them
Media Quality Summary Report The Media Quality Summary Report provides overall quality data for different endpoint types, including
Enterprise Voice peer-to-peer calls, Enterprise Voice conference calls, and calls that rely, at least in part, on the public switched telephone network (PSTN).
Server Performance Report The Service Performance Report lists the servers that have experienced the most problems, based on
measurements of such key quality metrics as degradation, packet loss, and jitter.
Location Report The Location Report provides a list of network locations and a summary of the media quality of the calls that
occur at each location. For purposes of this report, locations are based on IP subnets.
Device Report This report provides a summary of devices that are used for Enterprise Voice calls and it includes the average
media quality of the calls by device.
Call List Report The Call List Report provides detailed information about phone calls made or received within your organization.
Call Detail Report The Call Detail Report provides detailed information about phone calls made from or received within your organization.
In addition,here is a great blog taliking about improving the voice quality for your reference.
http://blogs.technet.com/b/nexthop/archive/2011/04/04/voice-quality-improvements-in-lync-server-2010.aspx
Hope these useful!
B/R
Sharon