Check your Acrobat preferences for "Display PDF in Browser".
The following also applies to FileMaker's interactive containers (unfortunately):
Display PDF In Browser
Displays any PDF opened from the web in the browser window. If this option is not selected, PDFs open in a separate Acrobat window. If you have installed both Reader and Acrobat, you can select which application and which version to use.
I am suffering from the same problem when running FM 12 in Windows 8, but experience no problems when running FM12 in Windows 7. Am eager to learn how to fix this if there is a fix.
Disabling and enabling Adobe Reader plug-in in IE worked for me, but now it takes at least 30 seconds to import a single page PDF file into a container field. Before, it happened really quickly.