Phones wont signin in after CA upgrade

Hi All,
I currently have an issue when Lync Phone Edition and Polycom VVX model phones wont sign in to our Lync 2010 infrastructure.
I see the Phone attempt registration, and just get an unauthorised message and stops trying, only a single time not like the Lync client get unauthorised the 3 times.
I have tried both via PIN Auth, and via USB connectivity same result either way.
I am looking at certificate as the cause, as we re-issued certificates to all Lync servers right before the issue occurred (new CA in the environment). 
A "Test-CsPhoneBootstrap" gives a success result, but when attempted from the phones nothing.
I have been checking the logs on the phones and can see some errors but not sure where to look next.
An Extract of the logs from the LPE device:
+++++++++++++++++++++++++++++++++++++
ERROR :: WebServices::CManagedWebRequest::ExecuteInternal: Webrequest failed with non-continuable error, hr=0x80004005
WARN  :: NModel::CCertificateProvider::GetDiagCode: Neither Ms-diagnostic or soap fault is found.
WARN  :: NModel::CUserAccountProfiles::OnEvent: Bootstrapper failed: status=3, hr=0x80004005, component will be stopped
ERROR :: NModel::CBootstrapTask::OnExecution: Error: hr = 80004005 - Failed to resolve user sip uri: phone=186!
+++++++++++++++++++++++++++++++++++++
And when tracing the UserPinService on the Lync FE
+++++++++++++++++++++++++++++++++++++
Component: UserPinService
Level: TL_VERBOSE
Flag: TF_COMPONENT
Function: TimedHash<T_V>.TimerCallback
Source: timedhash.cs(269)
Local Time: 12/10/2013-19:42:01.780
Sequence# : 00001B95
CorrelationId :
ThreadId : 16D4
ProcessId : 1068
CpuId : 2
Original Log Entry :
TL_VERBOSE(TF_COMPONENT) [2]1068.16D4::12/10/2013-08:42:01.780.00001b95 (UserPinService,TimedHash<T_V>.TimerCallback:timedhash.cs(269))(00000000005A137D)key :
[email protected]
+++++++++++++++++++++++++++++++++++++
I have seem some posts about factory resetting the phones for when the root CA has changed, we have done that and still nothing.
I have also seen the posts about updating the rootca store via the New-CsWebTrustedCACertificate, but from my reading of the set-cswebserviceconfiguration that InferCertChainFromSS is set to true (our server is) the
TrustedCACerts is ignored, so I don't think this would do anything as we should be downloading the certificate chain anyway..
Any ideas would be appreciated.
Cheers
Jason
My UC Thoughts

Hi,
Is there any other model of Lync phone in your environment? Does the issue happen for all Lync phone devices?
Please check your automatic configuration record as Lync Phone Edition cannot utilize Manual Configuration.
Here is a great blog troubleshooting Lync Phone Edition:
http://blog.schertz.name/2012/03/troubleshooting-lync-phone-edition-issues/
Note: Microsoft is providing this information as a convenience to you. The sites are not controlled by Microsoft. Microsoft cannot make any representations regarding the quality, safety, or suitability of any software or information found there. Please
make sure that you completely understand the risk before retrieving any suggestions from the above link.
Kent Huang
TechNet Community Support

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