For some reason they left in the Desilu logos, but not the Paramount ones. Anybody have insight as to why?
When CBS took over the Paramount TV library after the Viacom/CBS split, they started purging all of the Paramount logos and replacing them with CBS.
It's sort of like when Columbia's TV division took on the Sony name, and suddenly every single instance of a Columbia logo was covered up by a Sony logo.
Before 2006, season 3 generally wasn't tampered with, since the show's copyright was on the logo instead of in the credits. However, I do recall that when Sci-Fi ran the series, the Paramount episodes just had the 90s Paramount logo, with no copyright anywhere. That isn't as big of an issue as it used to be, but Paramount must have caught their mistake, because when the DVD releases started the next year, they made sure that every episode had an onscreen copyright notice, so season 3 had the old Paramount logo again.
When CBS took over the rights, they obviously wanted to make it clear that they were distributing the series, which is why they replaced the Paramount logos and reproduced the original copyright at the bottom of the CBS logo. Anybody remember back in 2006-07, when season 3 episodes even said "A Gulf+Western Company" under the CBS/Paramount logo?
Desilu has always been spared from these logo purges. Paramount/CBS never saw it as a conflicting with their brand identity. Some studios replace the logos of every entity they've acquired, others don't, and I honestly don't know why.