If this is an Adobe initiative, then "grrrr, thanks a lot". Or, is this something on our local end?
Lately we cannot open Excel (.xls or .xlsx) and Word documents (97-2003 or later versions) out of a PDF potfolio. We upgraded to Reader 9.4.6 and I think it was around that time (maybe even 9.4.5) that this ability went away. In the versions we have you cannot check "Allow opening on non-PDF....." as it is greyed out. Is this where you allow .doc and .xls files to open?
I too am having difficulty after upgrading to 9.4.6, but I am unable to open PDF files from my web browser (both Chrome and IE). If I edit my preferences and allow the PDF to open in the browser window, I can see them, but opening the application from a web page does not work.
Turning pop up blocker off/on does not make a difference.
Other files seem to open fine.