NM-B vs THHN amp capacity?
The current carrying capacity of wire and cable is determined by (1) the heat produced due to conductor resistance, (2) the high temperature limit of the insulation used, and (3) the surroundings of the wire to the degree it traps heat in the insulator (everything such as insulation thickness, conduit, proximity to a hot roof, etc.).  Items (1) and (2) are characteristics of the wire.  Item (3) is a characteristic of both the wire and the installation.

Even though the wires within NM-B cable are THHN wire and have insulation rated for 90 degrees C, many versions of the code, including 2011 NEC Section 334-80, limit ampacity of non-metalic cables such as NM-B to no more than that permitted with an insulation rated for 60 degrees C (probably due to heat retention by the thick outer PVC jacket, although they do not explicitly say that is the reason):


  334.80 Ampacity. The ampacity of Types NM, NMC, and NMS cable shall be determined in accordance with 310.15. The allowable ampacity shall not
  exceed that of a 60°C (140°F) rated conductor. The 90°C (194°F) rating
  shall be permitted to be used for ampacity adjustment and correction
  calculations, provided the final derated ampacity does not exceed that
  of a 60°C (140°F) rated conductor. The ampacity of Types NM, NMC, and
  NMS cable installed in cable tray shall be determined in accordance
  with 392.80(A).


The code goes on to explicitly describe how the cable must additionally be de-rated for the installation (multiple cables in one conduit, multiple adjacent cables in an insulated wall, etc, etc.)

The differences in ampacity are all about the effect of heat on the insulation.  Regarding multiple ampacities for a single wire type, there is always an asterisk somewhere describing the particular instance where the wire is to be used and which ampacity is applicable in that case.