It may come as a big surprise to you, but Visual Source Safe (VSS) has a tendency to corrupt PDF files. To fix this less-than-optimal default behavior, you simply need to add PDF as a Binary File. You can do so like this...
Tools -> Options
Click on the File Types tab, and add ;*.pdf to the list
Click OK
Note: We use VSS 2005. Your mileage may vary with other versions.