I am having similar issues. This feature has been in the Revit family as far back as 2008, and maybe further back. Where do we go now to modify the file locations? In the deployment files on our shared server, there are 2 Revit.INI files. These seem to be the likely place that these changes are made, but are they made to both files? To one, or the other?
Location:
\\OurServer\Revit2011-net\AdminImage\RevitSetup\RevitStructure\program files\Autodesk\Root\program\Revit.ini
\\OurServer\Revit2011-net\AdminImage\RevitSetup\RevitStructure\Revit.ini
When I ran this post by some Revit Support Technicians here at Autodesk they said Best Practices for Deploying Revit are covered in this AU course and to suggest you review it.
Let us know how things go.