I had one similar to that recently, there were actually two problems hopefully just the one for you. Factions Empathy/Initial World, when it updates the empathy change at the end of the mission.
And Best Path, it sets a best path if the mission was a loot and return mission. If the illegal, legal paths are screwed it can CTD.
I solved the Empathy/Initial World by going back through the values and found that I had doubled up some entries for some factions. The Initial world likes having simple numbers like 0.91, 0.65, 0.3, 0, -0.3, -0.65. Its best only to use these numbers. Make sure that everything is ok in MPnewcharacter.fl and Newplayer.fl.
The best path, was solved by simply removing a jumphole from the system. There's a limit on the amount a system can hold and this had apparently gone over it. Might have had a jumpthing created, then removed, then re added. FLExplorer (at least the older versions) dosen't delete the zone when you delete the jump thing. So you need to make sure that the zones get deleted other wise the goto Ar01, zone_Ar01_to_Li01,.. <----Would have more than one zone to go to.

it was a destroy all ships mission, and..uhh....what does the empathy/initialworld have to do with this? if its about new factions i havent added any......EDIT: bump.....BUMP

Edited by - [Chaos_leaderXiron on 8/3/2005 4:58:27 PM

Well, the problem that i had sounds similar and was due to factions. But, i had also had probs with best path at that time too. For my money, if it isn't faction reps and your sure of that its most likely the best paths or random_loot commodities. I doubt its the loot, but it is possible.
Does this happen everywhere or only within a new system? With every faction or just the one?

ive touched none of the loot properties (yet), and it only happens in my new system, but i've only got one faction set up for having missions against them, as its the only one of 2 factions that will mainly exist there. EDIT: bump -.-

Edited by - [Chaos_leaderXiron on 8/9/2005 12:14:45 AM

Its looking like best_path, did you add the system manually or by using FLE? If its done by FLE then it should have all of its paths done okay. Otherwise, its the kind of thing that you could get problems with.
Which factions are they?

i used FLE (although there IS a jumphole in my system that runs close to the route to the mission vignette...), and the factions are (currently, anyways) the Outcasts and the Bounty Hunters Guild (makes for some nice capship wars ;P ) EDIT: bump

Edited by - [Chaos_leaderXiron on 8/11/2005 1:41:27 AM

Well, could you try taking away the jump hole and doing the mission again? It might make a difference..