The two versions (tie-breaker using the Henchmen rating, and "no Arch-nemesis") came out at different point in the design process.
After a little internal debate, we settled that the version on page 5 (tie-breaker) is THE rule, while the one on page 12 is wrong.
Yet Fantasy Flight issues an official FAQ that states exactly the opposite (that Page 12 is RIGHT and Page 5 is WRONG).
Personally, I'm going with the FAQ. SOMETHING has to be recognized as the "official" ruling.