This is not a problem with Retina displays or with TPPG's configuration. It seems to be a bug in Acrobat XI under Windows 7 (64-bit). Several of my colleagues have encountered this problem at my workplace, which led me to find this thread. See here for another report of the same problem:
http://answers.acrobatusers.com/Printing-Comments-malfunctioning-huge-font-q191714.aspx