Intel's 3517UE @ 1.7GHz works x3 faster compared to another PC

Hello,

I'm using 2 PCs that has Intel's 3517UE @ 1.7GHz:

1. ADLINK's IBE2 (Com Express Type 2) http://www.adlinktech.com/PD/web/PD_detail.php?cKind=&pid=1235

2. Intense PC (http://www.fit-pc.com/web/products/intense-pc/)

The 2 PCs are booted with Win7-64

On the the 2 PCs we run the same exe file which comutes FFT radix 4 of 512 vectors each with 256 complex samples.

The Intense PC ends the computation 3 times faster then the IBE2.

How can we detect the difference between those 2 machines ?

Thanks,

Zvika