If you can travel to (enroll) and Edit Town on EA's Uni World, even if you aren't very fond of the place, I would have to say that it's the custom worlds themselves causing the problem, the method by which they were installed so that they behave as Uni Worlds should, or issues with the homeworld they are being transitioned into from. (ooh, I've just ended a sentence with not one but two prepositions and I'm too tired right now to fix that...)
Have you considered trying the NRaas Traveler mod, if you don't already have it in play? Seems odd that it would help with the world transitions in this case if you can't even Edit Town the custom worlds, but it certainly shouldn't make anything worse.
Can you install either of these worlds as if they were homeworlds (if this is possible) and start a game in them, or does that crash on you as well?
