There are two solutions to this problem:
A 'fixed' copy of the manual in .pdf format is available from www.mae.apple.com, which will print correctly with newer versions of Acrobat such as 3.0.
Alternatively, customers can install the earlier release of Acrobat from their MAE CD (manuals and Acrobat installers are in the /dox directory). This version reads and prints the Users' Manual file just fine.