Slight variation in NMR integrals of CH protons vs. CH2 or CH3
That's to be expected: Less protons as spatially close neighbours, less dipolar coupling, slower relaxation. 

For a relaxation/recycle delay of $\pu{1 s}$ and $T_1$ of perhaps $\pu{3 s}$, the Ernst angle is already only $44^\circ$, so your measurement is far from optimal anyway. Use a shorter pulse or longer recycle delay.

At one second, your are anyway dangerously close to generating echoes which overlay the signal from further scans, distorting the accumulated spectrum.