I was having problems with printing certain PDF's and it all started once I had installed some "new" updates through Microsoft and it changed some of my settings in Internet Explorer. Have you recently upgraded to the new IE9? If you have, uninstall it and it will take you back down to IE8. There are major problems with IE9 and it's compatibility with several programs. Microsoft is notoroious for wanting to get something NEW out there for the general public without testing it like it should and this is one of those cases.
PM me if you need anymore help and I can walk you throught some steps that might help because it will probably come up again in the future since not everyone out there that creates PDF's are using the same version of PDF maker through Adobe because its so expensive to upgrade anything Adobe related. I have been a computer tech/software tester for more than 20 years, so I don't mind trying to help out my fellow quilters when I can. Most of the time, the problems are an easy fix, you just need to narrow things down a bit and dig in to get to it!
Happy Thursday!!!