Some options are within the UserCfg.opt file ( %APPDATA%\Microsoft Flight Simulator\UserCfg.opt ). This file should not read-only.
But I’am not sure about whether the menu-animation-setting is stored within that file. Some settings are stored remote ( steam cloud ) and can be found in folder e.g. C:\Program Files (x86)\Steam\userdata\xxxxxxxxx\1250410\remote , but these are binary files ( except of the joystick settings ). That might be the case, if the re-installation was a real-full-reinstall ( manuall cleanup of AppData etc ) and the setting was then restored from the steam cloud. I would change the option in-game and check whether some of the files are updated.