I have read various posts here at StackOverflow regarding the execution of FFT on accelerometer data, but none of them helped me understand my problem.
I am executin
The low frequency artefacts are probably due to a lack of windowing. Try applying a window function.
The overall shift is probably due to different scaling factors in the two different FFT implementations - my guess is that you are seeing a shift of 24 dB which corresponds to a difference in scaling by a factor of 256.