SEP12.1.4013.4013 64 Bit Clients sylink.xml will not update

I currently have SEP12.1.4013.4013 impemented in a QA environment and we testing deployment with SCCM to update the sylink,xml file to move our machines to the correct groups.  Due to the size of the organization 157K endpoints we will be using SCCM2012 for this deployment.  All of the machine work great with the deployment except the 64 bit Server clients.  We have used the sylink drop tool and it says the file is updated but the file does not change in the directoryand it also states after the import the xml files was successful.  But it fails to update the file.  I first thought it was tamper protection but I ruled that out.  I tried the manual process of stopping the SMC service, deleting the select sylink files and then copying over the new sylink.  That process fails also.  So far the only process that does work is importing the communication settings directly in the client.  WIth 157K endpoints and over 5K servers virtual and physical we will not be efficient implementing one at a time on 64 Bit endpoints.  Has anyone else seen this issue in SEP12?