Why is the project “running” faster in the NetBeans internal terminal than on the Windows command line?

I am new to this forum, so excuse me if I am not asking the question correctly for the first time. I think that there is no need to specify the code, since I think this has nothing to do with the code, and the question may be more general.

I wrote and built a C ++ project in NetBeans 7.1.2 using MinGW (g ++) in Windows XP. Both versions of Debug and version Release work fine and provide the desired result of the calculations. However, if I “run” a project (or project) in the NetBeans internal terminal, I can measure the calculation time from 115 to 130 microseconds. If I execute an exe file on the Windows command line, I measure the calculation time from 500 to 3000 microseconds. (2.2 GHz Intel Core 2 Duo with 2 GB RAM. I measure time by reading the number of processor clocks from reset and dividing by the processor frequency.)
I tried the same thing on another computer (including project creation), also 2.2 GHz and 16 GB RAM and Windows7. The program works a little faster, but the template is the same. The same is true when I start a project from NetBeans, but in an external terminal (also in a Windows terminal). And this applies to both versions, debugging and release versions.

One of the calculations (not the most critical time) is the fast Fourier transform and depends on fftw ( http://www.fftw.org/ ) "libfftw3 -3.dll". Inside NetBeans, its location is known; at the windows dll command prompt, it should be in the same directory as the executable.

Why is it that the program runs much faster in the NetBeans internal terminal window than in the Windows command prompt window?

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, , Windows, NetBeans, dll ( ).

fftw_complex, double[2]:

for(int i = 0; i < n; ++i) {  

    double k1 = x[i][0] * (y[i][0] - y[i][1]);  
    double k2 = (y[i][1] * -1) * (x[i][0] + x[i][1]);  
    double k3 = y[i][0] * (x[i][1] - x[i][0]);  


    result[i][0] = k1 - k2;  
    result[i][1] = k1 + k3;  
}  

x y , [i][0] , [i][1] . result - .
5 513, NetBeans, 100 Windows. sehe.

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