He approached the Hendrix estate for permission to use the music. Alan Douglas, then Hendrix's musical curator, said they could do business if the movie was as weird as they said.
Mr Thompson showed him a rough cut of the film, shot in Alicante in Spain with a cast including the singer Ian Dury, comedian Billy Connolly and performance poet John Cooper Clarke. "Well, it's as weird as you say," came the reply. Permission granted.
But when the Hendrix family regained control of the musician's work last year and saw the finished Thompson film - a labour of love started six years ago - they were not happy.
Rumour has it the problem was the sex and violence, the culmination in "an orgy of madness, sex and death", to quote the publicity. A music industry source said: "They are very sensitive to the way Jimi's music is used."
Janie Hendrix, the late star's sister, was not specific. "After we screened the film, we decided it was not an appropriate venue for Jimi's work," she told The Independent. "Jimi's music contains powerful visions and we did not feel that what was portrayed in The Changeling was consistent with them." They were not aware any contract had been signed, she added.
So Mr Thompson was left with an unusable finished film. It had already been premiered with the Hendrix soundtrack at last year's Glastonbury festival. That was followed by a showing in Leicester Square, London, where it was snapped up by distributors who signed a deal to sell the film to Japan before going bust. When Janie Hendrix withdrew permission for the music this spring, it sealed the catalogue of problems that have plagued Mr Thompson's project.
"I was feeling a bit sorry for myself," Mr Thompson said. "The Hendrix idea had been there from the very start and inspired me all the way through. To have it taken away at the last minute ... And The Changeling is full of powerful visions. It's all very curious."
He was forced to consider alternatives to replace the music or abandon the project. He settled on a new soundtrack by JS Bach and Henry Purcell and the re-scored version should be finished by Christmas. A new screening will be arranged.
"It's absolutely fabulous," Mr Thompson said yesterday. "It's a completely different movie. For me, the Hendrix works fabulously but I was stunned by this new version. Luckily, the great thing about this movie is it doesn't date."
Despite all the difficulties, Mr Thompson, a former pop video-maker in his 40s, said he was not bitter. And at least he should now be able to pay those who gave their services in return for payment when the film was released, including royal wedding dress-maker, Elizabeth Emanuel, who designed the costumes. "It's a classic deferment movie, it's just been deferred a bit longer than normal. At least I think they will see it now. And I've still got the Hendrix. I can still see my movie as it was."