Holding down CTRL+SHIFT on either left or right does nothing. They are just extra keys (there is a term for them). You have to hit another input key. I have tried all kinds of sequences trying to toggle it back - obviously not the correct one.
It only affects the Notes window in the module. It is persistent for any game - both old saved ones as well as newly started ones, so it is somehow set in the module. I can even edit the module, delete the existing Notes Window, add a new one, and it still works right-to-left. However, it is only in that window.
It also affects my VASL "Info" window, which is the same VASSAL function (i.e., a 'Notes" window object).
Somehow it has set a flag somewhere that I can not see in any preferences and can not change.