Had the same issues with a 7525 on version 061.121.220.65000; an upgrade of the firmware to 061.121.224.18803 cured the issue.
Also made sure that on the Server 2012 R2 that ports 139 and 445 were enabled inbound/outbound on the Windows Firewall under advanced properties.
I saw that before I posted this and tried the suggested fix, but that didn't work. I called the Xerox support number and I am being helped by someone.
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I searched and followed everthing suggested here: http://forum.support.xerox.com/t5/Copying-Faxing-Scanning/workflow-scanning-on-75XX-and-57XX-Microso...
but still can't get a WorkCentre 7545 configured to use Workflow scanning using SMB to work with a Server 2012. Permissions are set correctly. The Xerox has firmware: 061.121.223.36000 and I applied patch 158499v1.dlm, but it's still not working. SMB port 139 is being used.
Any idea of what else to do? I have another Xerox (7435) working correctly using Workflow Scanning with the server.