I have the same issue using VMware View. With non-persistant desktops, each new machine generates a new hardware ID and creates a duplicate in SEPM. I've tried the link above to delete the HardwareID in the registry and the sephwid.xml file in the base image. It does not help. Duplicates still appear in SEPM.
Now that we're using SEPM 12, this causes a licensing issue. This used to not be the case with SEPM 11. We could have thousands of duplicate names, but SEPM didn't see it as a licensing issue.
Any suggestions?