The first instance of "The chickens have come home to roost" that a Google Books search finds is from C.A. Marvin, "Regulating Teeth," in The Dental Times (January 1868), and the chickens are unmistakably undesirable:
And now the universal law of compensation asserts itself ; a disordered stomach, a fetid breath, a loss of strength, all succeed, and the penalty of violated duty is inflicted upon the offending organs, the teeth. "The chickens have come home to roost." It is but simple justice. People will not see it, however. They wonder why they should have such poor teeth.
Further searching does turn up rare instances where the phrase appears to be used to refer to positive consequences or to consequences that are good for some and bad for others. In the purely positive category, we have this admiring article about South African entrepreneur Otto Mnyande from Enterprise 200 (1994) [series of snippets]:
Thandanani Foods. A Commitment to Ubuntu
The chickens have come home to roost for former sweeper, government clerk, sales rep and bold entrepreneur Otto Mnyande.
Umtata-based Thandanani Foods, frozen chicken wholesaler to Transkei's four million people, has a turnover of R2,5-million a month. The office of the Otto Mnyande, who once had to vacate a post of cardex clerk because of job reservation, is sparsely furnished with a tidy desk, displayed on which is a certificate of merit from the Transkei branch of the South African Black Social Workers' Association.
The certificate epitomizes the humane and skillful marketing strategy of this burly six-foot bearded businessman who saw a gap in the in the frozen food market and exploited it with borrowed money 16 years ago.
An earlier instance of similarly positive use appears in Christopher Sinsbaugh, Who Me!: Forty Years of Automobile History (1940) [series of snippets]:
Bill took the assignment seriously; in fact, he fell in love with the cyclecar idea, and his stories about the foreign development aroused interest in the tiny car and soon our engineers were playing with the idea. Bill, who even then was quite some designer, got busy with his pencil and published sketches of his ideas of what a cyclecar should be. These were inspirations for others who were working along the same lines, and soon one of Stout's chickens came home to roost. W. H. Mclntyre, of Auburn, Ind., who had been building motor buggies, gave Stout the assignment to design a cyclecar for him, which he planned to put on the market. Bill went to it and he drafted a job that met with McIntyre's approval. It was the Imp, first of America's cyclecars.
And in the positive-for-some/negative-for-others category, we have this instance from Michael Goldstein, "Re-Inventing Broadway," in in New York Magazine (May 29, 1995):
Securing tax breaks for new shows. No entertainment business can survive without new product. CBS Records, for example, learned this at some cost. In 1987, it was the industry king. The problem, though, was that CBS was minting money with two giant stars, Bruce Springsteen and Michael Jackson: old acts. Meanwhile, its main rival, Warner Records, had been busy launching new acts like Anita Baker and Madonna.
By 1989, the chickens had come home to roost: Warner had rocketed to a 40 percent market share, and CBS was down to 16 percent. Again, the analogy between Broadway and CBS (in 1987) holds: Where Springsteen and Jackson gave music executives a false sense of security, Rodgers and Hammerstein satisfies today's Broadway landlords while the guts behind the expensive façade slowly disintegrate.
But the negative examples are overwhelmingly more common, undoubtedly because the phrase "The chickens have come home to roost" arose from an older proverb: "Curses, like chickens, always come home to roost." The first unmistakable version of that proverb appears as an epigraph to Robert Southey's poem "The Curse of Kehama" (1810):
Curses are like young chickens, they always come home to roost.
Southey sets his poem in ancient India, but several mid-19th-century authors identify the proverb, in streamlined form, as being Arabian (G.C. Holland, The Millocrat, 1841) or Turkish
(William Sherwood, Self-Culture in Reading, Speaking and Conversation, 1855), usually giving it in this form:
Curses, like chickens, always come home to roost.
Nevertheless, a suspiciously similar saying appears in Chaucer, "Parson's Tale" (by 1400):
speke we now of swich cursynge as comyth of irous herte.
Melisoun generally may be seyd euery maner pouwer of harm Swich cursynge bireuyth euery man from the regne of god, as seith seynt poule.
And ofte tyme swich cursynge wrongfully returnyth a-geyn to hym that curseth. as a brid that turnyth a-geyn to his owene nest.
The origin of the proverb is thus uncertain. It seems quite clear, however, that the source of "the chickens have come home to roost" is "curses, like chickens, come home to roost"—and curses are extremely negative. Other things besides curses that (according to various 19th-century authors) "like chickens come home to roost" include lies, sins, wrongs, errors, evil wishes, taunts and sneers, "the lewd story or jest about women," restrictive immigration laws, politics, promises, thoughts, thoughtless radicalism, habits, and boys.
On the other hand, Geoge Burrowes, "Liberality Rewarded," in The Pacific Expositor, (December 1860) suggests a positive connection to homing chickens:
There is an old adage, "Curses like chickens, come home to roost." The same is true of blessings, deeds of kindness and benevolence.
But there is no evidence of a contemporaneous groundswell of support for the phrase "Blessings, like chickens, come home to roost."
Nevertheless, when the word curses drops out of the "chickens have come home to roost" expression, it makes a more benign interpretation of the phrase at least theoretically plausible.
The potential to view chickens coming home to roost as a good thing gained some ground when air force commanders (and others) during World War 2 referred to flyers returning from their latest mission as chickens coming home to roost. Among several authors who make this analogy is Rothsay Stuart-Worley, Letters from a Flying Officer (1982) [series of snippets]:
I search the sky; then suddenly I spot them, flying together lower and to the left of the first group of three. Thank God, they're all back safely ... all my 'chickens' have come home to roost: the happiest ending to the day. . . .
But the real tussle has only just begun. It will take time and a great deal of hard work before we finally drive the Germans from the air. There are a lot of stout fellows amongst them.
This usage obviously doesn't originate in the "curses" proverb, but it may have had some influence in softening the connection between chickens returning home and negative consequences.
Even before the war, the notion that returning to a familiar place is like chickens coming home to roost produced instances where the phrase did not imply a curse or anything negative. For example, From the April 6, 1920, address by President Chapman reported in "Wisconsin Jewelers Hold Excellent Convention," in The Jewelers' Circular (April 14, 1920), we have this paragraph:
You know there is an old saying that "chickens come home to roost." We have held our convention the last two years in other cities of the State, and while we have been treated most royally in these cities, we are glad to be back to Milwaukee. We kind of feel at home here you know. We have always found such a ready welcome from the jewelers of Milwaukee that we sometimes feel that we should meet here every year.
Ultimately, though, if you say or write that "the chickens have come home to roost," your listeners or readers will almost certainly expect that the chickens bear negative consequences of past misdeeds or indiscretions.