Idea: Maybe what's going on is, since fighters were never intended to be able to undock in the first place, perhaps being told to do so screws up their ability to accept future SEXP-induced AI goals.
This is a good theory. Maybe the goal code never registers the undock goal as complete. So, it would be hung up on the undock goal forever.
One way you could get around this is by using jettison-cargo-delay on the host ship. No undocking procedure required, and it's quicker too.
Whoa, I always thought that SEXP just set a ship's cargo to "none." I'll have to check that out.
EDIT: OK, Jettison works much more cleanly. However, it did not remedy the problem. In the process I have discerned the issue's true nature, however.
The problem is caused not by the ai-undock goal, but rather by the nature of how they enter the map. They're designated Beta, Gamma and Delta wings, but they don't show up in the wing monitor and nothing appears in the Wings command menu. As far as the game engine is concerned, their wings do not exist, so giving orders to said wing is rather pointless. Now, back to the problem of the fighters not accepting orders. The problem is, my SEXPs were giving goals to their wings, not each individual fighter. So, basically, this is still doable but you have to give each individual ship its goals and ignore the fact that they're all winged together. Problem solved, works beautifully (even if setting it up is a COLOSSAL pain in the ass).
Since giving goals to twelve fighters is more trouble than it's worth, I highly suggest making excellent use of the "initial orders" menu. So, to sum up:
Have the fighters start disabled and docked to the ship, with initial orders to do whatever you want them to do once they undock.
Have the fighters arrival cues set to 3 seconds after the mothership arrives, no warp effect.
Time events so that once the ship slows almost to a halt, it jettisons its cargo and all the fighters have their engines restored.
Enjoy. There's a slight problem in that each fighter experiences a miniscule bump upon disconnecting, but that's so minor I couldn't possibly care less.
VICTORY IS MINE!!!!!!

Thanks for all your help, folks!