They actually do not have different scales. (We do not have your code, so I am guessing here.) The locations of the peaks returned by findpeaks are indices unless you gave it the x-vector as an argument. You can get the x-axis values with the appropriate reference.
Example —
[pks,locs] = findpeaks(y);
x_peaks = x(locs);
figure(1)
plot(x,y, x_peaks,pks,'pg')
grid
See if that does what you want.
