difference of FFT.vi in FFT Spectrum (Mag-Phase).vi

Hi! 
I have 1 signal goes through 2 vis i got 2 differenct answer. FFT
spectrum(Mag-Phase) measures the magnitude and phase.. so does the FFT.vi
of the magnitude. However FFT spectrum brings me a postive magnitude
whereas FFT brings me some negative magnitude in some of the freq domians?
Whats the difference lies at? The FFT sample size???
 
I dunno.
 
Plase help