It looks like MS has released a fixed version of the Windows Server OS MP so the duplicate drive discovery issue should be resolved now. This highlights the importance of testing management packs before releasing them into your live environments.

This version is 6.0.7296.0 and is available for download here

Changes in this version

• In 2003, 2008, 2008R2 platforms, the mount point discovery script was also discovering logical disks as mount points which appeared to many as duplicates. These mount points for logical disks were removed to prevent confusion.
• In 2012, 2012R2 platforms, mount point discovery was causing rediscovery of logical disks and this rediscovery resulted in rules being run again. This was fixed.
• In all platforms, duplicate performance rules were shown for mount points and logical disks. This has been fixed.