[Non0Sequitur]

Ive tried the 'Update FreeSpace' button in the launcher, but it gives me an Invalid Patch File error, Yes i have the buggiest version ever

[Goober5000]

It's over 10 years later; they've probably taken down the update site.  You need to search online.
http://web.archive.org/web/19990421152550/http://www.parallaxonline.com/files/fs10x-106us.exe

[dANGER boy]

Goober5000, what did you do to fix the waypoint in that mission?  I want to go back and fix it, if possible, in the Galatea asteroid mission.  Did you just move the waypoint a little?

[Goober5000]

No, I changed the event from a "waypoint sequence complete" check to a "distance from final waypoint" check.  My modified events are the last ones in the missions I modified, so you can use them as examples.

[Mongoose]

I remember running into this bug occasionally back in the day, but I don't think I ever had it hit this hard.  I do remember that there was one of the fan-created missions included with Silent Threat that I was never able to complete because the one cruiser never managed to properly jump out at the end.  At least I finally know how to fix it.