The episodes on the DVD's are in order of production number - the order they put them in while filming. This is not necessarily the exact air order.
Not quite... I mean, if that were the case, then Scooter's introduction would probably be the first one on the DVD, the episodes are in broadcast order on DVD.
This is a problem with almost every single television series ever known to man: episodes are planned, filmed, canned, etc in a certain order, however, very rarely do the networks ever air them in that order. Most of the time, the episodes ARE aired in order in RERUNS, but for some reason, during the initial airing of the season, they're not always aired in order. A lot of it has to do with scheduling, certain months networks have what's called a "sweep", which I guess they really have to grab people's attention and interest because of more people watching TV or something, so they may air certain episodes that might seem more interesting to people during that time than what should come next in chronological order. And yes, there have been occasions where the pilot episode of the series isn't aired until a few weeks later, so in some of those cases, they are treated as "flashback" episodes when they weren't meant to be... that may or may not have been the case with TMS, those TMS was one of those shows that had separate pilots as opposed to just the first episode being dubbed "Pilot Episode" as is the case with a number of series.