I don't see any disagreement in the data, I think everything looks fine.
Except for one thing, maybe: the transmission of the pristine CNT should have integer plateaus, as you roughly have. But the "rounding" of the edges indicates that perhaps you have too short electrodes, or maybe even too small unit cell in the XY directions. Unless, that is, you simply have too few points on the black curve (fewer than for the blue and red). But it should really look like a step function, with the slanted parts.
I suggest you use 200 points or so for these plots, and check if the T(E) is really step-like for the pristine tube. But, otherwise in general, I don't see any problems.
