I already send a support ticket but maybe that this problem known to others too.
I didn't find it on the Forums so far.
Thats what i wrote to GOG
"Hi,
In the 3rd training mission, after a short time, the Game runs way too fast. ( I think more than twice the normal speed)
I restarted FS2 and played that mission again without problems.
However in the next, the first combat mission, it happened again.
I hope you can help.
Thanks Felix"
Is there a known solution yet?
Felix
Oops forgot to make this a question thread..

Try alt tabbing out of the game, then running the task manager.
Look for the FS2.exe running in the processes tab, then right click on it and select "set affinity..."
This should give you choices about how many of your CPU cores you want to work with that game.
I'm not really sure if that is your solution, but i did it with some other games that experienced something similar to what you're telling here.
I hope this helps, and as usual, did you try FS2Open already? it fixes lots of things in FS1 and 2.
Happy new year!

Thanks, I will try that Tab thing.
I didn't try FS2OPEN yet, but I will.
Felix

Stupid question, but did you try switching secondary fire mode (multiple missiles/single missiles) before it happened?
Hitting the wrong key will accelerate the game =)