Well raine is full of tricks to try to preserve it as much as possible, normally it survives a game reset, even a game load (loading a save state), and sometimes the test mode (but not always, depending on the way the ram is initialized or not). It's saved only when you quit raine or load another game, so if you go to test mode, and it's not detected because of a fancy ram initialization and then quit or load another game, you destroy the hiscore file.
Sorry I can't do much about that... !
edit : all this pushed me to update the very old code for this turbo key, it was still trying to display the fps as an int when returning to limited speed when it's been a double for quite a few years already, so the display was very wrong. Now it's correct, and it also displays the average fps reached while the turbo key was pressed (I reach more than 4000 fps during the sfad demo and with a debug build, but it's the assembler version, but it's really too fast at this level !). And finally it automatically disables the opengl double buffer while the turbo key is pressed, so now you can finally use this key without changing anything in the video settings !