I guess in both cases, it's the result of the mind adapting to a strange environment. Once the strange environment becomes the new normal, the old (previously normal) environment seems strange.

Probably in the first few days in the submarine or space station, it feels strange but you don't pay so much attention to the feeling because you expect it; it's unfamiliar in every aspect so there is no internal dissonance. After coming back, the old environment feels different and that seems strange since you didn't expect it to feel different; it creates a dissonance between your body/senses/subconscious and your conscious mind. Your conscious mind hasn't changed but your senses and subconscious mind did. Going back to the old environment makes the change within you seem more obvious since you have a conscious frame of reference to compare it to.

This is probably why the conscious mind finds itself observing the work of the subconscious mind with skepticism. There is probably some kind of loss of trust since the conscious mind observes that things don't feel the same as last time despite knowing that they haven't actually changed.