When Bewitched was first on the channel, they only showed the black-and-white episodes. In Nick at Nite's Classic TV Companion, it was said that they showed the black-and-white episodes because most stations had started with the color episodes. The books point out "you don't start reading Moby Dick at page 90" (or whatever). While it's great that Nick at Nite was showing long-unseen episodes, the book never really said why they skipped the color ones, and in fact it seemed to avoid acknowledging that fact (though the books episode guide only included the black-and-white episodes). Around 1998 there was a promo for the show, where an announcer said that the channel only aired episodes with Dick York, I think saying he was the better Darrin (I only saw that commercial once), but even if they were just showing favoritism, York was in four seasons of color episodes. I guess maybe Nick at Nite couldn't get the rights to the color episodes until 1998 (ironically only shortly after the promo mentioned above), but it seems they were trying to avoid saying they only had the black-and-white episodes. With the black and white episodes not being shown in syndication I guess those were up for grabs (when Nickelodeon began airing Looney Tunes the majority of cartoons they obtained the rights to were things other networks wouldn't touch - Speedy Gonzales, black and white cartoons, post-1964 shorts).
Ironically, Nick at Nite had a promo for the showanswering questions from fans (I assume the questions were made-up, but I don't know for sure). One question was "If Samantha is so powerful, why doesn't she do anything about Darrin's looks?" How ironic, considering most fans prefer York to Sergeant (and the promo didn't even make such a reference).
I find it ironic that once the color episodes were added, it seems the black-and-white ones were shown less. I know that the network pretty much showed every episode in order, and there were times when I saw several Dick Sergent episodes, missing some, and then after not watching the show for a few days or whatever saw that the color episodes with Dick York were shown. The gap between me watching wouldn't have been long enough for me to have just missed the whole first two seasons.
I heard that Nick at Nite did this to My Three Sons in the 1980s (I didn't have the channel at the time). Only the black and white episodes were shown, and then in 1998 TV Land aired only the color episodes at first, eventually airing black and whites as well.
And while on the subject of these channels only showing certain episodes of shows, it seems like when Happy Days premiered on the channel they only showed the first six seasons. The episode guide on the Nick at Nite website included all the episodes (I think the same can be said for Bewitched). I don't know if Nick at Nite just purchased half the episodes at first or if they didn't want to show those later episodes. I didn't know until later that a lot of fans dislike the post-Ron Howard years (but he was still a regular in season 7, which initially wasn't shown). The later episodes were added in 1997, and I thought they were good. Though I think some of the post-season 7 episodes were shown before then. I recall seeing the season 7 episode where Richie worked for a newspaper company once before all these episodes were added to the line-up, and I recall a 1996 promo for a Christmas marathon showing a clip from the season 10 Christmas episode (seeing that clip again a year later, I noticed it took place at the rebuilt Arnold's from season 7, and I think the clip showed either K.C. or Flip or both).
It was cool when Nick at Nite had marathons acknowledging the fact that more episodes of Happy Days and Bewitched were being shown. I was confused by the Happy Days one being called "Chacinated or De-Chachinated". Turns out the "Chachinated" ones referred to the later episodes, not neccessarily ones with Chachi, and thought it was odd that some of the episodes in the "De-Chachinated" hours featured Chachi (and I can't remember for sure but I think the "Chachinated" hours included some of the season 10 episodes without Chachi).