Each Module/Window can have it's own preferences. Each Module/Window inherits preferences from the previous Module/Window loaded into TeSSH. TeSSH keeps track of which options have been changed from the inherited values.
So, in some sense, rather than storing the absolute preference values for a Module/Window, TeSSH stores the differences between the Module/Window and the inherited preferences.
If you click on the drop-down arrow in the upper-left portion of the Preferences window, you will get an advanced menu of options:
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