Last week’s disqualification of “Alone Yet Not Alone” from Oscar’s best song category is the latest in a series of scandals and head-scratchers that have plagued the music Oscars for years.

It’s only the second time in four decades that a music nomination has been withdrawn. The last time was in 1972, when composer Nino Rota’s Oscar-nominated score for “The Godfather” was declared ineligible after it was learned that his love theme was written for a 1958 Italian film.

The “Godfather” score was replaced by a new nominee, John Addison’s music for “Sleuth.” Curiously, the winner that year was the score from “Limelight,” Charlie Chaplin’s 1952 movie, which became eligible by getting a belated Los Angeles release in 1972.

Rota wound up winning the Oscar two years later for his “Godfather II” score, despite the fact that a great number of those themes could be found in the earlier score, making most of the work “not original” — and in fairly obvious violation of Oscar rules. So even on Oscar night, the head-scratching over strange choices in the music categories is a familiar phenomenon.

In the case of “Alone Yet Not Alone,” the title song of a low-budget, faith-based film, composer Bruce Broughton was taken to task by Acad governors for sending emails to friends in the music branch that asked them to consider his tune (written with lyricist Dennis Spiegel and featured prominently in the film, set during the French and Indian War).

Broughton, a former Acad governor, insisted he didn’t ask anyone to vote for the song, but rather that they listen to and consider it. “I’m devastated,” he told Variety. “I indulged in the simplest, lamest, grass-roots campaign, and it went against me when the song started getting attention. I got taken down by competition that had months of promotion and advertising behind them.”

Acad president Cheryl Boone Isaacs on Feb. 1 told Variety, “Every year we review the awards season process in every way, to modify, clarify, improve, and to do whatever is needed for more clarity. It all comes down to the integrity of the awards process. Everything changes constantly, including the business, the ways of communicating and the rules. We’re always trying to be in front of the situation to keep the integrity of the awards process at its highest level.”

An additional nominee in the category will not be named.

“Alone Yet Not Alone” was No. 57 on the three-hour, 15-minute DVD mailed to branch members. About 20 of the films on the list were recognizable titles; the majority were little-seen or talked-about (from films as far flung as “Kamasutra 3D” and “3 Geezers!” to “The Muslims Are Coming!” and “Jewtopia”).

This is a system the branch instituted several years ago to create a level playing field for the many songs entered, most of which have no promotional budget to garner attention at awards time. For the first few years, there were actual screenings of the songs used in the films in Los Angeles and New York; now the Acad simply sends a DVD to everyone, and asks them to watch and vote.

And, according to Oscar rules, the choice is not just supposed to be a good song. Voters are encouraged to choose based on “effectiveness, craftsmanship, creative substance and relevance to the dramatic whole.”

Statistically speaking, voters prefer songs that are performed as part of the story. Of the 19 songs nominated in the previous five years (2008-12), 11 were performed oncamera and only two were end-title songs. This year, four of the five were performed oncamera, including the “Alone” song.

The unknown factor is how many members voted this year. “This absolutely reeks of low-voter participation,” said one music exec. “There is no way a significant number of people got together and decided (‘Alone Yet Not Alone’) is Oscar-worthy.” Some estimate the turnout may be as low as 50 or 60, not the 100 to 150 that had been estimated in earlier years (the branch consists of 240 composers, songwriters and music editors). The Acad refuses to disclose voting totals.

The music branch’s song choices have been the subject of frequent complaints, and their methods for determining the nominees subject to constant tweaking in recent years. During four of the past eight years, fewer than five nominees were chosen (in 2011, there were only two; in 2005 and 2008, just three).

And major songwriters and performers have been ignored on multiple occasions. This year, for example, widely promoted entries by the likes of Taylor Swift (“Sweeter Than Fiction” from “One Chance”), Coldplay (“Atlas” from “The Hunger Games: Catching Fire”) and Lana Del Rey (“Young and Beautiful” from “The Great Gatsby”) were bypassed.

In 2011, it was songs by Elton John (“Love Builds a Garden” from “Gnomeo & Juliet”) and Mary J. Blige (“The Living Proof” from “The Help”). In 2009, it was Karen O (“All Is Love” from “Where the Wild Things Are”), in 2008 Bruce Springsteen (the title song from “The Wrestler”). Twentieth Century Fox’s longtime music director Alfred Newman, a nine-time Oscar winner, used to complain that “everybody knows their job, plus music.”

If only the Academy could figure out how to honor it without repercussions.