It happens all the time, In many games. I have not found one yet that it does not happen in.
It happens before I hit any key in the config menu. It is also happening outside of the config menu (Missile Command example). If I hit another key say down arrow, the game accepts it, but then continues to do the up arrows.
I have tried rebooting, re-extracting, running from command line, running from Game Launcher, disabling all background tasks first, disconnecting the keyboard, disconnecting IPAC, disconnecting sidewinder joystick. Nothing has made a difference. It happens only in .66, not in any other application that I have tried.