Sometimes it crashes after the first skirmish or during the second, and occasionally as early as during the first skirmish, but that's only in the debug build.
On the regular one, it seems to crash only after the second shivan skirmish, but I can't tell if it's as I'm approaching the Trinity or not. I haven't gotten close enough to see the initial pink(fuschia?) blip on my scope in several builds. It's usually just before, during, or just after Zeta 1's communication after the second shivan skirmish. I don't know how much help this is, though. I do know that the 3.6.7 release version doesn't have this issue. This is starting to feel like it felt when I was helping Ambrosia Software track down a CTD bug in Escape Velocity Nova (I'm on the beta team for what should be the final update for that game). Play it till it crashes, send a report, crashlog, etc. Get another build, try again, send a crash report, ad nauseum.