If it helps, here's how I just fixed this problem:
(Backup your files before doing this)
1) I looked at the event viewer and got: Product: Microsoft Lync Server 2010, Web Components Server -- Error 25542. Failed to find node: /configuration/system.webServer/security/authentication/windowsAuthentication in XML file: C:\Windows\system32\inetsrv\config\applicationHost.config,
system error: -2147020584
2) Went onto the front end and found the C:\Windows\system32\inetsrv\config\applicationHost.config file.
3) I found this section:
<windowsAuthentication enabled="true" useKernelMode="false">
<providers>
<add value="Negotiate" />
<add value="NTLM" />
</providers>
</windowsAuthentication>
And I disabled it by turning it into this
<!--
<windowsAuthentication enabled="true" useKernelMode="false">
<providers>
<add value="Negotiate" />
<add value="NTLM" />
</providers>
</windowsAuthentication>
-->
4) I found the section it spoke about in the error:
It looked like this:
<authentication>
<basicAuthentication />
<clientCertificateMappingAuthentication enabled="false" />
<digestAuthentication />
<iisClientCertificateMappingAuthentication />
</authentication>
5) I added Windowsauthentication like this:
<authentication>
<basicAuthentication />
<clientCertificateMappingAuthentication enabled="false" />
<digestAuthentication />
<iisClientCertificateMappingAuthentication />
<windowsAuthentication />
</authentication>
6) Did an IISReset and ran the installer again and it worked fine.
