You could manually change the axes labels. You may refer to the gca function which returns a handle to the current axes in the current figure. You may also try adding the following lines to manually change the axes labels on the EMD plot:
%Add the following lines after the EMD function call
a = 5083:5093; %time vector
ax = gca; %fetches handle to EMD plot
ax.XLim(1) = 0; %adjusting x-axis to start from 0
ax.XTickLabel = num2cell(a); %manually changes the x-axis labels
