I know this isn't much help, but I use Vista Home Premium, and it does that occaisonly. It will do exactly the same, even though it's FSX-SE, not just FSX.
Normally, a simple "cold" boot (power off reboot, not just a "warm" boot where you click Reboot) will stop it doing that. On my system. I always reccomend a "cold" boot. Warm boots are notoriously unreliable as far as clearing problems like that.
What causes it, I have no idea, but if it does it, and i want to keep doing other things, I just close it with the task manager, and go on about my business, rebooting when I feel like it. It doesn't do it every time, just on rare occasions. What causes it, I have no clue. I suspect it's a problem in the FSX executable someplace.
I just wanted to let you know, you aren't alone, but to me, it's a small thing, easily dealt with. No help at all, but there it is...
Pat☺