...Different Destinations - S3-E5
Trivia: While they're waiting for the Venek Horde to attack again, when John is chained to the statue, Harvey/Scorpius is playing the harmonica with his feet up on John's lap. Notice that both soles of Harvey's red boots have the name "Andy" written on them. In "Toy Story" Woody's boot has "Andy" written on its sole, and here in John's mind it's to signify John's ownership of the neural clone.
Chosen answer: It's never explained. John mentions a theory that his less technologically developed craft simply interferes with the wormhole less than the "superior" Vipers, but they never make a concrete determination on that point. But we also have to take into account the fact that Moya traverses wormholes with no ill effect as well.
Garlonuss ★