Like lots of folks in my age group, I watched Star Trek incessantly in syndication during the 70s.
Is there any evidence that season 3 was not included in some syndication packages? I remember seeing shows from the first two seasons over and over, but most of these season 3 shows, I saw only once, and I would not be surprised if there were a few that I never saw.
The graphics are blue only on season 3, correct? I remember barely seeing that.
Maybe I was simply playing outside on the wrong days.
It's my understanding television stations require series have "X" amount of episodes before they are interested in buying them for syndication. Which is a 100 episodes. (ST was just shy of that.) So I can't imagine any station only broadcasting two of the three seasons. In my days I saw the third season as often as the other two.
As far as I know, all three seasons were always syndicated. A lot of fan favorite concepts came out of that year: IDIC, Gem, Surak, Tholians, etc. I saw the third season often enough, but my local station aired all of the episodes wildly out of order for a long time. Your timing may have just been off. I often catch the same damned episode of certain shows when I tune in randomly. I'll never pick a winning lottery number, but I'd get "Planet of the Amazon Women" when I'd tune into a Buck Rogers rerun.
Generally speaking, the episodes all came as a package and the local stations showed them all. They did frequently air in random order, though. When I was eight years old, I recorded all the episodes from syndicated broadcasts and for whatever reason, they went an entire year without running The Enterprise Incident, Requiem for Methuselah, The Savage Curtain, and All Our Yesterdays. And then someone noticed and they ran all four on consecutive nights. Then, I recall WPIX in New York having periods where they made an advertising point of running them in production order and then airdate order. Did they do that in other markets in the '80s?