System Identification Toolbox "Frequency Function"

When using the System Identification interactive tool, why does the Frequency Function Data window (the transfer function estimate) only start at higher frequencies? 

I made a simple example of two phase shifted 10Hz sinusoid waves. The Periodogram (FFT squared) shows data from 1 to 200 Hz, but the Frequency Function Data only starts at 10 Hz. Since the Frequency Function is just the ratio of the FFTs, it should go down to 1 Hz.

The problem is that I have a large data set (motor current to angular velocity) where the input is sin-swept (chirped) from 1e-5 to 400 Hz, and the input and output FFTS definitely include low frequencies (see attachment plots). But the Frequency Function Data only starts at 100 Hz, and this is confusing. Also, the phase is incorrectly peaking, so something odd is up.