(A certificate chain processed, but terminated in a root certificate which is not trusted by the trust provider.

I was deploying a Lync Server Director in a Multi-Tenant configuration after i assigned the certificate a went to start the services, the Front-End services couldn't start with the following errors

Log Name:      Lync Server
Source:        LS Protocol Stack
Date:          3/12/2013 1:52:06 PM
Event ID:      14397
Task Category: (1001)
Level:         Warning
Keywords:      Classic
User:          N/A
Computer:      Lync Director FQDN
Description:
A configured certificate could not be loaded from store. The serial number is attached for reference.
Extended Error Code: 0x800B0109 (A certificate chain processed, but terminated in a root certificate which is not trusted by the trust provider.).
Event Xml:
http://schemas.microsoft.com/win/2004/08/events/event

">
 
   
    14397
    3
    1001
    0x80000000000000
   
    58
    Lync Server
    Lync Director FQDN
   
 
 
    0x800B0109
    A certificate chain processed, but terminated in a root certificate which is not trusted by the trust provider.
    AD5CEFED0AA77CC23B0B247DCF82F208
 
========================================================================Log Name:      Lync Server

Source:        LS Protocol Stack

Date:          3/12/2013 1:52:06 PM

Event ID:      14359

Task Category: (1001)

Level:         Error

Keywords:      Classic

User:          N/A

Computer:      Lync Director FQDN

Description:

Unable to use the default outgoing certificate.

Error 0x800B0109 (A certificate chain processed, but terminated in a root certificate which is not trusted by the trust provider.).

Cause: The certificate may have been deleted or may be invalid, or permissions are not set correctly.

Resolution:

Ensure that a valid certificate is present in the local computer certificate store. Also ensure that the server has sufficient privileges to access the store.

Event Xml:

http://schemas.microsoft.com/win/2004/08/events/event

">

  
    
    14359
    2
    1001
    0x80000000000000
    
    59
    Lync Server
    Lync Director FQDN
    
  

  
    0x800B0109
    A certificate chain processed, but terminated in a root certificate which is not trusted by the trust provider.
  

I installed an Inetermediate CA certificate from the certificate provider and the Front-End Service started successfully, the strange thing is that I didn't face this issue with the Front-End servers so I was pulling my hair out and looking into different directions!!