Problems after upgrading to acrobat reader 9.3

Yesterday, I noticed that my pdf's were not being loaded by the plugin. I could see a Windows process for acrobat that was hogging my CPU but it just sat there and the PDF never loaded. I upgraded my acrobat from 8.0 to 9.3 and now the PDF loads, but always in it's own window. It does not load inline with the wiki page contents. Additionally, my PDFs do not load at all in IE8 anymore.