Make sure your popup blocker is disabled in both the IE Tools -> Internet Options -> Security tab menu as well as under Tools -> Popup Blocker - sometimes the one under Security settings will be left on and functional even though the other is turned off.
In the Reader, go to Edit -> Preferences -> Internet, and take the check out of Allow Fast Web View, OK out.
If neither of these work, go back to the Security tab in IE and change Display Mixed Content to Enable.
Generally this is a last resort for me - set the IE security to Low to see if that is hindering you, then disable the most likely offenders until you see which is the one that allows the .pdf to display.
Good luck.