This matter is certainly an irregularity. The only other Element that exists from a storyline perspective is the combination of all of them (Ultima). The mechanics of the Junction System of VIII shed a lot of light on what Holy and Ultima are from an elemental standpoint (as does Crystal Chronicles in regard to Holy, it essentially being a combination of Fire, Earth, Water, and Wind, as well as those Elements most closely associated with these).

Ultima is as powerful as it is for a reason, as it is raw Spirit Energy (refer to the Ultima section of this document), which may be what any such non-Elemental attack utilizes. Neo Bahamut's attack may be Spirit Energy fired in a raw form, rather than diluted or broken down into one of its seperate properties (as Shiva or Ifrit's attacks would be).

Assuming that Ultima Beam is likewise a blast of Ultima, perhaps in linking an Elemental Materia to one of these Materia that utilize raw Spirit Energy/Ultima/the combination of all Elements, that specific property of the Ultima attack is nullified, absorbed, or diluted. Granted, according to this theory, some of the Spell's Elemental properties should roll on and still cause damage to the character no matter what, and even in VIII, Ultima itself could not be absorbed, but perhaps those incidents in which it was totally absorbed involved more than one such link of Ultima-type Materia with Elemental Materia?

What think you, masamune?