I suspect it is a browser problem more than anything... What version of IE are you using?
There are some message boards online that do address PDF issues with various versions of IE, here are a couple:
Microsoft Q&A: http://bit.ly/1mSWmWS
Windows Club: http://bit.ly/1wtHPDi
Keep in mind if browser settings are the culprit it's pretty much up the end users to update their own settings on IE, so there won't be much you can do, unfortunately.