How come the DVDs aren't released in episode order?

It's because of the copyright issues for the movies featured on the show. When movies were featured on the MST3K during its original broadcast, Best Brains (the production company that made the series) would negotiate the terms in which they were allowed to use each movie. Generally they were allowed the complete rights to show the movie on TV but they didn't always get the rights to release the movie on video. Since the idea of releasing the entire series on home video didn't seem very likely during the days of VHS, this was not a major concern for Best Brains. It wasn't until the advent of DVD that the idea of releasing all of MST3K on home video even seemed viable. This also remains an issue for modern streaming services, since TV rights don't carry over to streaming rights. Today, Shout Factory, who releases MST3K on DVD, has to renegotiate the rights to each movie with the copyright holders of the original film and pay them a license fee. Some episodes may have license terms that are too expensive or simply unavailable for Shout Factory to purchase, and this makes releasing MST3K in order nearly impossible.