I think that although Empire of the Sun was a far superior film, 1941 probably did better money wise. With John Belushi, Dan Aykroyd and some other big names, 1941 I would think made more money at the box office. Eventhough it didn't do well, Empire of the Sun is still one of my favorite movies.
I checked out
1941 at the IMDB and it says the film's runtime is 118 minutes, but that the director's cut is 146 minutes. I never knew there was a director's cut of this movie. Is that what you purchased?