For starters, are you sure they are PDF's? Can you supply a link to one for us to look at?
Also, what version of Reader are you using and what is your OS?
This had been an intermittant issue for me too (Reader 10.0.1, windowsXP). I solved by going back to Adobe Reader version 9 which for me does not have this issue and works fine. Might have to google around to find v.9.