CHiPs changed from a theme featuring a great brass band sound to some disco electronic crap for the last 3 or 4 season. BTW, any news about this on DVD? I know Ponch could use some cash.

This is perhaps not what you were looking for, but the theme song for the first episode of Popular was different. The show opens as the singer is sitting on wall (IIRC) and singing the song, as if it's a music video. The camera then pans into Sam McPherson's house and the episode begins.

The song actually survived as the closing song for every other episode; it was replaced with that Kendall Payne song for the opener.

Going back a ways, Double Trouble (84-85) revamped the show completely between its two seasons and changed theme songs. Both songs can be found as .wav's at the linked site (it's true you can find anything on the internet).

Again, it is not a different song or words added to an instrumental as the Original poster points out.

Did you know that the same people that performed the song appeared as a Beatles like rock band (The Mosquitoes) in an episode?

You might be thinking of DS9. They didnt really change it but redid it with a different tempo.
Space 1999 changed from the first to the second season.