Zac,
In doing some testing within 9.3.1, 10 and 10.1, where you print to a .pdf file from within ArcReader. I am including the work flow for you, and in all 3 versions of ArcReader, this options seems to work. Gracias!
ArcReader>open a .pmf>file>print>check on "Print to file">Ok>Enter the path where the file will reside and include the .pdf extension for the name.