I too have had the same problem. I'm replaying the campaign for the first time in a couple years. I never had a problem with the original install, but that's long gone. I'm trying to get this thing to work on the RC2 3.6.10 build and the 3.6.10 media VP's. I was running just fine with no errors until the mission right after Sync activates the first time. I show up and my wingmate shows up, but only half of her ship. Really weird looking to have only half a herc. I flew in behind her just to see what it would look like, and I saw details in the cockpit I'd never noticed before. (Nice attention to detail btw, whoever did that model.) And then, I fly to the node as instructed, but my subspace drive never enables.
ctrl-shift-s in the Tech Room is working for me, though.