Your description is not quite clear... first you say "when I go to the settings panel it gets flipped to false (reflecting the correct starting state)" then "why isn't it getting set to false"?
If the starting state is false, it will always start as false. There is nothing to "flip" it. It's just how it starts. Note that if you use groups (non-zero group ID) then your checkboxes become radio buttons instead.
That's funny, I thought it was pretty clear.
I have a Debug.log message in a start method that shows the UIToggle is false, when it should be true.
I even put the UIToggle up the top of the script execution order list and it still shows true.
It's only when I accessed a panel that actually has the widget with said UIToggles on it does it get set to false - without me actually touching it.