zero padding shifting signal peak?
The FFT of a strictly real input signal is conjugate symmetric.  What that means is that, for a single sinusoidal frequency, the FFT result includes not just one positive frequency peak, but also a another peak at the negative frequency.  For signals that are not strictly integer periodic in the FFT length, the peak can be a very broad Sinc after zero-padding.  For extremely low numbers of signal periods (and for frequencies that are very near Fs/2), the negative frequency peak is close to and thus can interfere with the positive frequency peak and distort its exact location.

So, for very small numbers of periods that are not known to be strictly integer periodic in aperture, it may be better to use a parametric estimator of some sort, rather than an FFT, even windowed or zero-padded.