I have this exact same issue. If I have Internet Explorer open already when I click a link from an email or shortcut, it will open in Acrobat Reader just fine. If I enable the IE plugin and open PDFs in the browser then things work fine as well. The problem only occurs when opening PDFs from a link straight into Acrobat Reader as we would prefer to do. I have tried the newest version of Acrobat reader as well as the old Adobe Reader 11. Both had the same issue.