Spells Only Do What They Say They Do
While "[i]n general, positive energy heals the living and hurts undead creatures" (PH 311), some rare positive energy effects that inflict damage don't also heal the living. For example, the 6th-level Clr spell bolt of glory [evoc] (SpC 35-5) launches a "white bolt of hissing positive energy" that can only inflict damage.
It's best to adjudicate whether a positive energy spell that inflicts damage also heals damage based on the spell's description rather than making that in general a constant.