I have managed to reproduce it in notepad. It doesn't happen when typing (probably because notepad uses the repeat events, which do not seem to be firing?), but the problem is visible with the alt key. Key down on alt will display underlines under the shortcut keys for the menu items, and key up will then highlight the first menu item (File). When I tap quickly tap alt, the shortcut underlines are displayed, but the menu item is never highlighted.
The fact that there are no repeat events seems strange. Are those generated by Windows, or the keyboard driver?