More specific rules override less specific rules. The whip is an exception.
#1) No it isn't an exception. Where does it say that it is an exception?
There is the GENERAL rule that weapons do a certain #D whatever upon a successful strike.
There is a more specific rule that the whip deals no damage on a successful hit against a foe with a +3 nat armor bonus or a +1 armor bonus.
But there is an EVEN MORE specific rule that the whip with the Flaming enhancement does 1d6 fire damage.
Why is it more specific than the rule about whips? Because there is the "Set of All Whips," which contains (obviously) all whips. Then, within that set is the "Set of Magical Whips," within which is the "Set of Magical Whips with Special Abilities," and within that, the "Set of Magical Whips with the Flaming Special Ability"- and some other subsets besides...
#2) Hyps' formulation of the problem essentially violates the principle that a weapon that deals 2 kinds of damage can damage a target that is not immune to both. Here, the second type is magical fire.
#3) It seems to me, and to others, that the reading of the Flaming power is being tortured. Some feel that the damage is being done by the weapon, not the enchantment. "A flaming weapon deals..." has been much discussed, but read on.
Once more:
Flaming: Upon command, a flaming weapon is sheathed in fire. The fire does not harm the wielder. The effect remains until another command is given. A flaming weapon deals an extra 1d6 fire damage on a successful hit.
The second sentence of this entry reads "
THE FIRE does not harm the wielder"- not "
THE FLAMING WEAPON." This matters. They have already made a distinction between the weapon and the power granted by the magic. "A flaming weapon" is nothing more than a description of a weapon wrapped in a shroud of magical fire. And if the wielder tried to kill himself with this weapon's flames, he would fail.
#4)Furthermore, ignoring the fire damage because of the armor/natural armor problem with whips would also violate p28DMG- "Certain types of damage, however, should never be nonlethal damage...such as fire"
However- one thing I think we can ALL agree on is:
Don't use your Vorpal Whip against Trolls unless its a Flaming Vorpal Whip.