You may see the error, “Lync has both per-user and per-machine instances installed. Click OK to remove the per-user installation.” The error occurs every time the Lync client is launched.
This is caused when a user has downloaded and installed the Lync Attendee User-Level Client, and then installs the Lync client. This is bound to happen because the Lync Attendee client is freely available on the web (http://www.microsoft.com/downloads/en/details.aspx?FamilyID=68a3ca04-a058-4e47-98ea-9e9af7ebd6e3), but the Lync client is not.
Remove the Lync Attendee and it fixes the problem.