I am not getting a minimum frequency since I installed the new software today. I have run 1v as amplitude for Lyme treatment as suggested by Dr. Stegmann's document. I see the 1v and the frequencies are in red, which is also something new.

The problem here is the mark on "Swap Frequencies+Amplitudes for Out1 and Out2". If you unmark it, then all is correct with the freqs. But if you mark it, then the program doesn't apply the parameters you set on the freq limits pane.

So, until this issue is resolved, unmark its box. If you need to swap the channels, you can swap physically the connections (if using SC).
The red numbers are to indicate that you have selected that feature.

For more details, please check the link:
http://www.spooky2.com/forums/viewtopic.php?f=5&t=4868