This is a known limitation - you say it was working in your previous version - so which version are you upgrading from?
Here's how we got around this situation. I added two properties to the netlist.prp file, PART_NUM_TOP and REV_TOP. Then created a scout config file that copied the PART_NUM & REV propertiy info to the PART_NUM_TOP & REV_TOP properties. I made two of these config files, one that only updates the properties and another that does the cross referencing and updates these properties. This way the user has the flexibility to do what is needed for their situation. Hope this info is helpful.
We were still using the 95 version of Logic due to contractual obligations. I have finally got the permission to update to the latest version using PADS Designer. But we had several custom scripts to automate some of our common tasks. I have never dug deep into them, so maybe it didn't work then either. But as gedeakins suggested above they may have done something similar to correct this issue.
Thanks for the comment. I have done some scripting but not when it comes to PADS and/or Dx. Is it possible that you could share this scout config file?
I wouldn't go down the SCOUT route, SCOUT is no longer under active development and the cross-rerencing functionality is being replaced by the built in cross referencing. The simpler though less elegant solution is to add a couple of new properties and place those on the sheet. The user will then need to keep the values in sync from the Borders dialog page (Setup - Settings - Project - Borders and Zones)
See the videos on managing borders if you need further clarification Design Creation