I don't know if PDFs do this but one time a OSX user gave me a quicktime file that didn't work.

It turns out that the codec was part of the mac file "resource" and stored in the filesystem rather than in the file. When the file was sent over FTP the codec didn't come along with it.

It turned out that the "cp" command line program on OSX did not copy the resource data either. In order for the resource data to be copied the file had to be copied using the GUI.

I copied the file using "cp" and compared it using "cmp" and "diff" in addition to "md5" (or "md5sum"). Neither of these commands showed any difference in the file but the copy would not play on the same Mac that the original file played on.