Both results are correct. Please read the embedded online help, chapter "Understand FastHenry2 output":
The result 
Computed matrices (R+jL) 
 Row 0: n1 to n5 
 Freq = 10000 
  Row 0: 0.00343966+1.59836e-009j 
 Freq = 100000 
  Row 0: 0.00343966+1.59836e-009j 
 Freq = 1e+006 
  Row 0: 0.00343966+1.59836e-009j 
 Freq = 1e+007 
  Row 0: 0.00343966+1.59836e-009j 
 Freq = 1e+008 
  Row 0: 0.00343966+1.59836e-009j
  
All impedance matrices dumped to file Zc.mat 
This is the actual impedance of the square loop, for each frequency. You can see that the result is in the R+jL form, that is, the real part is the resistance and the imaginary part is the inductance. 
The results are also dumped to the file Zc.mat. Note however that in this file the results are in the R+jwL form, where w is the angular frequency, that is, 2wf and f is the frequency. 
Best Regards,
Enrico