I just spent about six hours solving it, and it's one of the most obscure bugs I've ever come across. It was caused by WMC's giant commit of features back in August 2008. Here's the eureka moment from IRC:
[03:23] <Zacam> So, what the **** was he _trying_ to do there?
[03:23] <Goober5000> he was being too clever by half
[03:24] <Goober5000> he was checking for warp distance to complete the warp effect
[03:24] <Goober5000> problem is, the warp effect is governed by time, not distance
[03:24] <portej05> umm... is that really a good idea given warp is time, not distance?
[03:24] <Zacam> Which regular DIDN'T NEED.
[03:24] <Zacam> ****.
[03:24] <Goober5000> so in this mission, Alpha 2 warped in but he was DISABLED, so he didn't go the distance expected
[03:25] <Goober5000> which mean he never stopped arriving
[03:25] <Zacam> fffffffffff
[03:25] <portej05> argh!
[03:25] <Zacam> So, how in the hell does that add up to not being able to warp out?
[03:25] <Goober5000> which meant he never executed his AI code (which wasn't really noticeable because again, he was disabled)
[03:25] <Goober5000> and because he never executed the AI, there is NO SHIP in the mission that executes AI (the player doesn't count)
[03:26] <Goober5000> which means that ai_process never executed, which meant waypoints were never created
[03:26] <Goober5000> and since waypoints were never created, the distance check never succeeded
[03:26] <Goober5000> and so the player's warp was never restored
[03:26] <Zacam> Well ****.
[03:26] <Goober5000> that's like an eight-link chain of dependencies there :p