Hello,
I assume that the probe has a cap of 10pF, which is comparable to the cap in LC. Probing will detune the tank, and moves it out of the resonance, thus the Rp value, calculated with this method is off. Best way to confirm this is to try impedance analyzer, or do full math on the circuit wit the probe.
Why are you concerned with the true Rp value? In all applications we have worked with, it's irrelevant, i.e. there is no difference whether you process true Rp value or ADC code.