From the Wikipedia entry:
The original title credit theme to Thunderball was entitled "Mr. Kiss Kiss Bang Bang," which was written by John Barry and Leslie Bricusse. The title was taken from an Italian journalist who in 1962 dubbed agent 007 as Mr. Kiss Kiss, Bang Bang. The song was originally recorded by Shirley Bassey, but was later rerecorded by Dionne Warwick, whose version was not released until the 1990s.
Writes Geoff Leonard in "Bond by Barry: The Story of James Bond Music": For Thunderball, the fourth film in the Bond series, the producers for this outing felt it a good idea to do away with the normal title song, ("Thunderball" was thought to prove difficult lyric-wise in any case). So they decided to use the name by which Bond had become known in Italy and Japan - Mr Kiss Kiss Bang Bang. Accordingly, Barry based the entire score around this title song which had lyrics written solely by Leslie Bricusse (Newley was working in America at the time). The Bond team had even chosen the singer - Dionne Warwick, who sang her own arrangement, after Shirley Bassey's original version had failed to impress.
Barry takes up the story: "Dionne's was a marvellous song and she did a great arrangement for it. It was a really strange song. I had about twelve cow bells on it with different rhythms, along with a large orchestra, and thought it a very original piece. Then, at the last minute they got cold feet and decided to have a song called 'Thunderball'." The official reason for the change of mind was that the original song-title may have been considered to have sexual connotations in conservative America, but rumour has it that there may have been a threat of court action from Bassey following her replacement by Warwick. Obviously if the song wasn't used at all, there could be no case to answer!
Whatever the reason, it led to Barry's long partnership with lyricist Don Black, as by the time the decision to change the song had been taken, Bricusse had also gone to work in America and wasn't available. When director Terence Young heard Tom Jones singing Thunderball for the first time, he said it sounded like 'Thunderfinger'. Barry's laughing rejoinder was to the effect that "I gave them what they wanted."
"Mr. Kiss Kiss Bang Bang" was removed from the title credits after producers Albert R. Broccoli and Harry Saltzman were worried that a theme song to a James Bond movie would not work well if the song did not have the title of the film in its lyrics. John Barry teamed up with lyricist Don Black and wrote "Thunderball," which was sung by Tom Jones who, according to Bond production legend, fainted in the recording booth when singing the song's final, high note. Jones said of the final note, "I closed my eyes and I held the note for so long when I opened my eyes the room was spinning."