Original viewers of The Shining sat down to watch a psychological horror movie about a man who holes up inside a snowbound hotel, loses his marbles and tries to kill his family. Three decades later, the joke's on them; they read the whole thing wrong. The Shining is actually a Holocaust movie in disguise. Scratch that: The Shining is, in fact, Stanley Kubrick's version of Theseus and the labyrinth. No, wait: it's his veiled apology for helping Nasa fake the moon-landings, or a vast history lesson in human evil, from the dawn of man to the end of time. If there were ever a film to send the viewer mad, The Shining fits the bill.

Director Rodney Ascher estimates that he used only 10% of the interviews he conducted for Room 237, his riveting documentary on The Shining and its afterlife, presumably for fear of getting lost in the maze. But those that remain are creepy enough. Disembodied voices rear up on the soundtrack, each with their own pet theory, their own lurid conspiracy. These witnesses know Kubrick's film back to front, inside and out. They want to tell us about the "secret window" in Ullman's office, the significance of the number 42, and "the mysterious Bill Watson", a lowly hotel factotum who may just be CIA. After a while, most alarmingly of all, the voices start to make a kind of sense.

Ascher cobbled Room 237 together on a thrift-shop budget, editing at home, at night, after he'd put the baby down to sleep. "I cut the film between the hours of 8pm and 3am, and those hours are perfect for breeding a certain paranoia. I would listen to all these interpretations and think, 'Well yes, but no, but maybe.' It was like opening the book of Necronomicon or falling into quicksand."

Judged purely on face value, The Shining was Kubrick's adaptation of the Stephen King bestseller. It starred Jack Nicholson as Jack Torrance, a struggling writer and reformed alcoholic who takes a job as winter caretaker at a haunted hotel. On its initial release, the film was widely seen to have fallen between two stools. The Shining was too arty for the horror fans and too trashy for the Kubrick buffs. Even King had his issues with the film. The novelist felt that Nicholson was too obviously demented as Torrance, that this hobbled the drama and that Jon Voight should have played the role instead. Room 237 shows him the error of his ways.

It would be nice to dismiss Ascher's subjects as a gaggle of idiotic, excitable fan-boys with too much time on their hands. Annoyingly, the shoe won't quite fit. Geoffrey Cocks, who sees the film as a Holocaust parable, is professor of history at a Michigan college. Bill Blakemore, who decided that the film was about the genocide of the Native American, after spotting a carton of baking soda in the background, is a senior correspondent at ABC News. These people are educated, articulate and often plausible. Yet somehow The Shining has infected them. Compelling, claustrophobic and cross-referenced to within an inch of its life, Room 237 depicts Kubrick's film as a kind of cinematic petri dish. Conspiracy theories bloom like mushrooms in the dark.

The BFI is releasing a restored, extended cut of The Shining, so I take myself to a preview screening. Rather worryingly, the film strikes me as somehow richer, stranger and more visceral than it did in the past. Part of this is the simple bonus of seeing it on a big screen. Part, I fear, is down to Room 237. Barely 10 minutes in I'm starting to understand where the theories are coming from, as little Danny (Danny Lloyd) pedals his bike past forbidden room 237 and the pristine ghost-girls invite him to "come play with us for ever and ever". The trouble with Kubrick's film is that it is so meticulously well composed. It has such ridiculous depth of focus. One has the sense that everything in these crowded frames (pictures on walls, cartons on shelves) is there for a reason, throbbing with significance. Watching The Shining is like scrutinising a painting by Richard Dadd or a malign version of Where's Waldo? Stare too long and you lose the plot.

But how many of these kinks have been put there intentionally? When a hack director makes a continuity error, it is taken as proof of incompetence. When a revered genius does the same, we wonder what they meant. The Shining comes riddled with bungled cuts and jarring locations. A chair vanishes from its place by the wall while a sticker disappears from a bedroom door. Midway through, the typewriter changes colour.

Ascher speculates that Kubrick may have been having some fun, teasing his audience, though he concedes that some of the cuts may just be mistakes. He is particularly intrigued by the hotel carpet that reverses its pattern from one shot to the next. "That's the trickiest one, because it means moving the camera's orientation from one end of the set to the other. That's a huge operation. It implies real intentionality."

No doubt many of the more outlandish interpretations could be confirmed by simply speaking to those who worked on the film. Yet Ascher deliberately chose not to go down this route. He wanted to keep his focus on subjective responses as opposed to objective truth. "In any case, even if you know the intention of the author, it doesn't necessarily make sense of it all." The unconscious, perhaps, is the great unsung hero in any work of art.

Undeterred, I ring up Jan Harlan, Kubrick's brother-in-law and executive producer on The Shining. Harlan is happy to correct a few misconceptions. No, he tells me, the film is not an apology for faking the moon landings. That rumour was partly seeded by a French TV documentary that aired after the director's death in 1999 and appears to have been doing the rounds ever since. He says that he still sometimes receives outraged letters about it: "How could Mr Kubrick have done such a thing?". Harlan tuts in exasperation. "He didn't, of course. But the story is still going on."

Regarding the continuity errors, however, the jury is out. Kubrick, he explains, was always intent on pushing the form, on leaving the work open to multiple interpretations, like the French impressionists or the Cubist painters that went before. "A straightforward horror film was not what interested him," Harlan insists. "He wanted more ambiguity. If he was going to make a film about ghosts, he wanted it to be ghostly from the very first to the very last. The set was very deliberately built to be offbeat and off the track, so that the huge ballroom would never actually fit inside. The audience is deliberately made to not know where they're going. People say The Shining doesn't make sense. Well spotted! It's a ghost movie. It's not supposed to make sense."

Whether this will provide comfort for Asher is anyone's guess. While assembling Room 237, the director found himself watching The Shining again and again, his brain whirring, his senses in uproar. Inevitably, he came away with a theory of his own. "There's a scene in which Ullman says that Grady stacked the bodies in the west wing of the hotel," says Ascher. "I thought, 'west wing'? That sounds like the White House. The Kennedy assassination. All of that." He's got to move on; he has to break free. I have a mental image of him still stuck inside that haunted hotel, still wandering the reverse patterns of the hallway carpet, in danger of playing for ever and ever.

• Room 237 is out on 26 October; The Shining is reissued on 2 November.