Assignments of reference designators (refdes) are typically performed somewhat randomly in the Packager engine, and updating based on board placement in the layout application. Many companies would like to assign reference designators based on the placement within the schematic document, providing a simple way to locate the component in the schematic.
DxDesigner does provide some reference designator manipulation for formal reuse blocks, but not for informal reuse blocks (circuit copy) or more general sheet-based assignments.
Here are a couple of scripts that can be used to assign reference designators based on the schematic sheet.
There is a document included in the attached zip file that describes how to use the script in detail.
The RefdesPrototype2007 scripts work with EE2007.3+ flow
Feel free to enhance the scripts and share those enhancements with the community.
RefDesPrototypePADS_DX is the PADS and netlist flow version.