I made 2 short flights with FS2004, but none of these things happened. Touchdowns and fuel cuts were registered, pause feature is working as well.
1. I made 2 very short flights, of < 10m between 2 closely located airports. Maybe longer flights cause some issues. But so far FS2004 is the most correctly responding flight sim. Prepars and X-Plane provide sometimes not quite reliable data.
2. I have Win 10 and will need to install VM for Windows XP and check flight sim in that environment.