Why did the Gilligan's Island theme song change between seasons?

According to TV Series Finale, there was a stipulation in Tina "Ginger, the movie star" Louise's contract stating that she was to be the last person billed in the opening credits. After Louise's contract was signed, the parts now known as "Mary Ann" and "The Professor" were recast to Dawn Wells and Russell Johnson respectively. This casting change, combined with Tina's contract, required them to be placed in the end credits.

According to this Today Show interview (YouTube, @ 3m 30s) with Dawn Wells and Bob "Gilligan" Denver, Denver explains how his own contract stipulated that he could choose his own billing. Before season two began, he declared to the powers-that-be that unless Wells and Johnson were added to the beginning credits for season two, he would move himself to the end credits. The change was made; either Tina Louise agreed to the credit sequence alteration, or her contract was reworked.

Interestingly, this interview was the first time Wells was made aware that Denver's demands were the reason the theme song was changed.

I also witnessed a second variation of the song, which only took place during re-runs. Some syndicates re-running the show manipulated the second half of the theme song, which ran during the end credits. These broadcasts silenced the audio when the words "each week" were sung, transforming

{...} so join us here each week my friends {...}

into

{...} so join us here {SILENCE FOR TWO BEATS} my friends {...}

I presume this was done since the re-runs were broadcast on more frequent intervals than weekly, and the associated networks questioned the intelligence of the viewership.

Additionally, The Gilligan's Island fan site hosts an alternate theme song played during the pilot episode.

I know of no other variants.

I met "The professor," Russell Johnson, at one of Andrew Ramage's Twilight Zone Conventions in 2002 or 2004 (he starred in two classic TZ episodes), and I asked him about "and the rest" in Season 1 of Gilligan's Island.

He told me that the producer had already commissioned the theme song and the singers before all the characters were finalized and the song had already been recorded. Gilligan, the Skipper, the millionaire and his wife and the movie star were already characters in the original script. There would be more characters, so the song ended "and the rest."

Johnson was promised that he and Mary Ann would be mentioned when the new song was recorded for Season 2. And they were.

I heard similar explanations but I like mine the best. The original theme was done "...and the rest". Well the show is only going to last one season anyway.... And it didn't end.

Well, Dawn Wells and Russell Johnson (who through the years when writing to each other signed their cards and letters "the rest") went to Sherwood Schwartz about changing the song. Sherwood said......well let's just say this is the first time the words "pound sand" were heard. But the answer was NO!.

Now I am telling this because of Bob Denver. Bob always played doofuss characters. But in real life he was well educated (I recall he was a teacher at one time), and was no coward bottom line: DON'T MESS WITH GILLIGAN.

Thinking that it was not fair he goes to see Schwartz. Again Schwartz said NO!

Well Bob just happened to have his contract in his coat pocket (yeah, just 'happened to'). He brought it out and showed Schwartz a certain clause stating that Bob gets his name anywhere he wants. So he tells Schwartz he wants his name last! Of course he'd be willing to negotiate that with Schwartz - maybe they could come to some middle ground - like The Professor and Mary Ann instead of the rest, and...

he'd keep his position in first place.

That story always gives me a warm feeling in my heart.

The theme changed because the actors who played the professor and Mary Ann were unhappy that they were referred to as "the rest", so they demanded that their character's names be added into the theme.