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As explained in the following technical article, it might be that the .PMF file was saved with an absolute path name:
FAQ: Can broken data links be repaired in a .PMF file when viewed in ArcReader?
You might try these steps:
1. Open the map document you would like to publish, in ArcMap
2. Select the File menu > Map Document Properties
3. Choose the "store relative pathnames to data sources" option > Apply > OK
4. Save the map document
5. Create a new folder in the desired output location for the published map
6. Select "Publish Map" from the Publisher toolbar drop-down > Name the .pmf > Save
7. Select "Create data package" from the publisher toolbar in Arcmap > Navigate to .pmf > Open
8. Select the General tab of the data Packaging dialog > Select the data package Location browser and navigate to the pmf folder location
9. Under the data Format pane, select the 'Copy data in existing format' option > OK
10. A publisher Message appears > Ok
11. Close Arcmap
**You should now be able to access the pmf, with data links intact
I hope these steps help.
Thanks for the response & sorry to just now give my solution to this. I found that if the zipped folder was not manually unzipped, that is if the folder was automatically opened when downloaded, the data links were broken. When going back to the downloads folder (Windows 7) and specifically extracting the contents, all paths were preserved.