I have had exactly the same problem myself.
I posted a support question here:
http://discussions.apple.com/thread.jspa?threadID=2572401&tstart=0
but it's been totally ignored by the apple folks. I also reported the fault via the "bug reporting" but it's just been ignored.
If you open the PDF in Preview, then re-save and re-sync, the fault sometimes goes away, but doesn't cure it happening in the middle of a big presentation 😟
Let me know if you get any response,
Dave.