I don't have FS2, and can't download it at the moment with my dialup internet, so for the past few years I've been playing FS1 w/Silent Threat expansion pack.
Now, if any of you have modded in Silent Threat, you'll notice that every time you save a mission that the game tells you that "this mission contains silent threat ships and you can't play it with base Freespace" message. I get this even when I don't add any Silent Threat ships! Is this a real problem or just another pointless FRED error message? Can you still run those kinds of missions on base Freespace?