This is good advice, and I did actually have to extend the permissions also. However this was not the overall problem. In fact I opened a ticket with Citrix and we did a Webex and they noticed that the Schema had in fact already been extended with our previous version of Presentation Server, so that was not the issue at all even though I was lead to believe that by the error messages I received. The CentralStoreRoot folder which had been added to Active Directory was some how corrupted and was not allowing the Password Manager install to complete. What he ended up doing was deleting the CentralStoreRoot folder from the Program Data\Citrix folder in Active Directory. Then we re-ran the Schema update and the Domain update from the Installation CD on the Domain Controller which is the Schema Master and both finished and the CentralStoreRoot was recreated and the installation liked it this time and completed. Then I was able to run a "Configure and Run Discovery" from the Citrix Access Management Console and everything was successful. We do not know why the folder had become corrupt, maybe it was associated with the fact that we are now on XenApp and running it so many times perhaps mangled the attributes, but it is not clear and it was over all remedied which is all that really matters now.
Thank you for your time on this. There are many areas with the Schema updates that a person needs to check regarding permissions on the Schema Master and in fact 'allowing' Schema Updates as you had mentioned.
