I am trying to use a fast fourier transform to extract the phase shift of a single sinusoidal function. I know that on paper, If we denote the transform of our function as T, th
The phase value in the result bin of an unrotated FFT is only correct if the input signal is exactly integer periodic within the FFT length. Your test signal is not, thus the FFT measures something partially related to the phase difference of the signal discontinuity between end-points of the test sinusoid. A higher sample rate will create a slightly different last end-point from the sinusoid, and thus a possibly smaller discontinuity.
If you want to decrease this FFT phase measurement error, create your test signal so the your test phase is referenced to the exact center (sample N/2) of the test vector (not the 1st sample), and then do an fftshift operation (rotate by N/2) so that there will be no signal discontinuity between the 1st and last point in your resulting FFT input vector of length N.