why can't I compare two .pdf files?

Two versions of the same document, both output as .pdf from the same tool. Readable, commentable, printable … but when I try to compare them [Acrobat X Pro, 10.1.4] I get the vague message "Acrobat could not compare the documents completely", which actually turns out to mean "Acrobat was unable to spot differences clear to the naked eye, anywhere in the document."
Has anyone found a simple trick to get this useful function working? Thanks in advance for hints and tips.