Really? Unless your Damage Resistance says that it has an exception against magic it should stop it. Stoneskin for example gives DR against all except adamantine, so I don't see any problem here.
It's not supposed to work that way.
...So how is it supposed to work? Never played Pathfinder before, so I'm just going on from what the game tells me. In-game it is consistent at least.
Well, for starters 2d6 bonus damage is equivalent to Holy, or Bane. So it's a tremendously powerful damage bonus, on par with some of the most powerful enchantments in the game.
Secondly, the damage is from an enchantment, so it's not weapon damage.
Thirdly, the damage is untyped per RAW, which implies that it's force damage or energy damage. If it was physical damage it almost certainly by typed, like slashing, etc.
You could definitely interpret it as plain physical damage, but that's plainly not how the enchantment is supposed to work.
If it did work that way, it would be better than Holy, or Bane, or any other enchantment, as it's 2d6 against anything, with an easily avoided damage penalty.
That's why most of the sources I found ruled that it isn't blocked by DR.