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