Actually, on the 1980s prints, we used to see this Paramount TV logo:
(short peak version)
(tall peak version)
Some of the episodes used the filmed version of the logo, but most others from the period used the videotaped version also seen on the first two seasons of
MacGyver. In any case, the 1979 version of the Lalo Schifrin jingle was heard over it.
Yes, it is true that in regards to the season 2 episodes beginning with "A Piece of the Action" (in broadcast order), on syndicated prints the early 1968 Paramount "Rising Circle" was replaced by its successor logo:
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As the series was syndicated in 1969, I can't help wonder whether or not the "Closet Killer" logo (with the Dominic Frontiere or Lalo Schifrin jingles) was seen at the end of ST:TOS before?
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~Ben