FFT funciton for vibration data

Hello,

I am working on vibration experiment. I got a data from a vibration sensor and I am trying to compute the FFT for that data. The experiment run several times and the period was different for each time, for example first run was for 3 minute and the second run was 30 second. Now I want to divide the run into equal samples but I have problem with that: I run the following code for all sample:

Fs = 1000;       % Sampling frequency

num_samples=length(yvect); % yvect is my data
figure
NFFT1 = 2^nextpow2(num_samples); 
Y1 = fft(yvect,NFFT1)/num_samples; 
f1 = Fs/2*linspace(0,1,NFFT1/2+1);
plot(f1,abs(Y1(1:NFFT1/2+1)))

The output will be

but when I choose to divide each run to 1s ( 1000 sample ) then I got strange plot from FFT.

and I also saw some people using Y1 = fft(yvect - mean(yvect))/num_samples; and when I use it, it will give noting in the FFT plot. and what is the purpose from using it.