I've run into a problem where my character wants to start running backwards and I'm limited on what I can press to either pause to menu / resume game, tab+shift to a different program in Windows, autosave, or close the program. After the program closes, my keyboard cannot even type anything on other Windows programs, and I am left with the hasty option of having to restart my computer.
This is a very strange problem. Windows does have a few shortcuts for accessibility functions but they result in a loud beeping sound and a pop-up when triggered, so usually you wouldn't be hitting them without knowing.
If the keyboard has its own custom drivers and/or configuration software forth you should try updating or reinstalling the drivers to see if that fixes it. You could also try a different keyboard (if you have one on hand) to determine whether this behaviour is specific to that keyboard.
Failing that you could try setting the game to run in fullscreen windowed mode, which might fix your problem and will also make switching to other programs more seamless.
To do this go to the installation folder (C:\GOG Games\System Shock 2, or wherever you installed it to) and edit cam_ext.cfg
Go to the force_windowed entry and remove the semicolon in front of it so it just looks like
and save your changes. This will make the game run in a borderless fullscreen window (assuming the in-game resolution is set the same as your desktop resolution).