From the help of that function you will see that the output S should be:
0050 % S (spectrum in form time x frequency x channels/trials if trialave=0;
0051 % in the form time x frequency if trialave=1)
0052 % t (times)
0053 % f (frequencies)
0054 % Serr (error bars) only for err(1)>=1
Therefore the correcter way of displaying the spectrogram would be:
pcolor(t,f,S.'),shading flat,colorbar,xlabel('time'),ylabel('freq')
HTH
