TotalTerminal closes valid terminal windows when launching/injecting

When I restart the computer or re-log in, TotalFinder will close any active stand-alone terminal window the application originally launched with. This happens when TT launches/injects itself into the terminal application. For example, I restart and the main terminal app first launches and shows my old open terminal tabs. When I find that my total terminal binding isn’t working, I launch the total terminal app. It ends up closing the stand-alone terminal window and opens an empty TT window. This a big problem for me b/c the window in question often has multiple tabs I need, chock-full with debug information and individual history of recent commands that I might need to re-issue.

Is there a way around this? This a big drawback for me.

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I have checked the 1.4.11 code and the code handling this flag is still there:

defaults write TotalTerminalDoNotTouchWindowsOnStart -bool yes