I WILL BE HAPPY TO GIVE YOU A LONG-WINDED ANSWER! Sincerely! I love explaining things! I will even OVER-EXPLAIN things! Seriously, I have a job interview in a couple hours and this will honestly relax me. So yes, I'm about to write way more than what you asked. In fact, it's embarrassing how much I am about to write on this subject. It'd probably be better to just go on sctvguide.ca and get the answer yourself. Still want to read my post? Okay, it's your funeral:
There are three series of SCTV:
Second City TV (The first 3 seasons)
The original, half-hour series as aired in Canada; syndicated in America
SCTV Network 90 (Seasons 4-5)
A 90-minute version, produced by and aired on NBC. The vast majority of it was new material, but in order to fill time they sometimes included repeats of old sketches from the original series. It was later retitled to just "SCTV Network"
SCTV Channel (Season 6)
a 45-minute version made for Cinemax.
All three of these shows are popularly known as simply "SCTV," furthermore they were all syndicated into 185 half hours. So the 90 minute shows and the 45 minute shows were all cut up and rearranged and turned into half hours. These 185 syndicated half hours are what the bootleg DVDs consist of. For a lot of people, this IS the complete SCTV; I gather very few people were privy to all three original incarnations of each SCTV series. One would have to live in Canada for Seasons 1-3 and then move to America for Seasons 4-5 (I believe Season 6 aired in the same format in both countries; seasons 4-5 aired in an shortened format in Canada).
The DVDs (Volumes 1-4) are of the NBC incarnation of the show, in their original 90 minute format. The show used a lot of licensed music and also included musical guests, and Shout Factory cleared MOST of it, but some things had to get edited out. Most of them are relatively minor in the grand scheme of things. And chances are, the syndicated versions of the shows are just as edited... I know for a fact that a lot of stuff didn't make the cut for the syndicated versions. But I want them still because I'm a crazy completist, and the chance there might be SOMETHING included in the syndicated version that isn't included on the DVD is enough to make me want to check them out. Also, I like some of those half-hour shows even though they are entirely composed of material from other, longer shows (the half hour version is almost always how the show gets played on TV when it DOES show).
Shout intended to release more comprehensive volumes of SCTV, but they wound up dropping it. They DID release a box set called "The Best of the Early Years" which was comprised of 3 Season two episodes and 12 Season 3 episodes. Not so much a best-of, more like a "here's the 15 least expensive episodes to clear." So that means all of Season 1, the vast majority of Season 2, and a lot of Season 3 is unreleased. None of Season 6 is released, either.
From what I understand, the thinking was Season 1 wasn't as funny as future seasons, and starting with the NBC shows could be a logical alternate start-point. Since the early NBC shows feature a lot of repeat material, they also serve as a best-of. But the first three seasons are classic in their own right and a lot of fans consider them to be much better than the NBC shows.