The Root store highlighted in this page is woefully outdated, however it seems that this is reality.  I need to talk to a program manager who provides the s/w portion for Lync handsets to people like Polycom as significant updates are required to the Lync system to allow it to work effectively with Lync Servers.  Please see this page as an example and note that I'm trying to also make contact through the Microsoft Root Program team.  - no luck so far.

http://technet.microsoft.com/en-us/library/gg398270(v=ocs.14).aspx

An update in April 2013 was made to replace the CyberTrust Root.  Were others updated?  http://support.microsoft.com/kb/2855339/en-us 

Kind Regards
 
Steve Roylance
 
GlobalSign
steve.roylance@globalsign.com
 
Springfield House, Sandling Road, Maidstone, Kent, ME14 2LP, UK.
Tel: +44 1622 766766  Fax: +44 1622 662255
Follow the GlobalSign Conversation

That can be frustrating.  Of course it's not the hardware vendor, it's the Microsoft firmware. 

I would suggest looking at phones such as Polycom's VVX500 series and other phones for Lync that use Polycom's firmware.  They may be more flexible, or at least easier to deal with when it comes to this.  http://blog.schertz.name/2012/11/importing-certificates-polycom-ucs/ 

Of course, for the phones you already own...

Edit: Just noticed you work for GlobalSign and this may be about getting your own certificates included, updated, or acknowledged.  I'll leave my previous comments here for others.

Are you having an issue with a specific Root Certificate? The trusted Root Certificates had a big update in January 2014. Make sure your Lync Phone Edition devices are running firmware of 4420 or greater.

In my reply to: http://social.technet.microsoft.com/Forums/lync/en-US/23b36e4f-a5c7-4e6c-a521-4567ddddfd77/lync-phone-edition-polycom?forum=lyncdeploy I mention some Root Certificates are not listed on the TechNet page as of yet but are working.

Edit: GlobalSign is one of them.

An update in April 2013 was made to replace the CyberTrust Root.  Were others updated?  http://support.microsoft.com/kb/2855339/en-us 

Hi,

The link above is for Lync online and may not apply for Lync on-premises. Also you can see CyberTtust Root certificate is still supported for Lync Phone in the link:

http://technet.microsoft.com/en-us/library/gg398270(v=ocs.14).aspx 

Best Regards,

Eason Huang