I tried repackaging Acrobat XI with both AAMEE and APTEE, but I found that you need a specific customization wizard for Acrobat Pro XI. After repackaging it from scratch and including the Reader plist file, the issue is not resolved.
Link with detailed deployment info: http://resources.jamfsoftware.com/documents/white-papers/Administering-Adobe-Acrobat-XI-Pr o-with-the-Casper-Suite.pdf