As far as I can see there are no discrepancies, you just have to carefully read and use both rules.
The rule in the Core Rulebook, as Are mentioned previously, says
Are wrote:
"Some abilities and spells ... bestow permanent level drain on a creature. These are treated just like temporary negative levels, but they do not allow a new save each day to remove them."
The Energy Drain ability from the Bestiary is one of those, although it only bestows negative levels if a condition is met (failing the next day's saving throw).
So both rules, don't contradict each other.