The Seleka "are playing us," said one military official.
The official described the Seleka as a "mafia" that is trying to curry favour with the Americans even as the rebels extort local villagers and engage in illicit trade with Kony's fugitive fighters.
About 100 US military advisers are deployed across four countries to guide the international campaign to catch Kony, whose brutal militia, the Lord's Resistance Army (LRA), has raped, abducted and killed tens of thousands of people over the past three decades.
After first sending US forces to central Africa in 2011, US President Barack Obama must decide next month whether to reauthorise the deployment and extend it for at least another year.
Some senior US military leaders have been lukewarm about the mission, citing its duration and the fact that Kony does not pose a direct threat to American interests.
But the operation still draws strong bipartisan support on Capitol Hill, and many expect the White House to stay the course.
"For 30 years, this individual has been creating mayhem and some of the worst atrocities on the continent," said congressman Edward Royce, chairman of the House Foreign Affairs Committee.
"Now is the time to double down and see the counter-LRA mission to the end."
A Ugandan guerrilla with a messiah complex and an uncanny survival instinct, Kony has eluded capture despite the best efforts of the Pentagon and the State Department, which is offering a US$5 million reward for information on his whereabouts.
Although Kony is still on the loose, US officials and backers of the mission cite several measures as evidence of progress.
The estimated number of LRA fighters in recent years has dropped by more than half, to fewer than 200. Four of Kony's senior commanders have been killed or captured.
Reported civilian abductions have fluctuated but dwindled overall. Tens of thousands of villagers who fled the LRA have returned home.
Paul Ronan, project director for the Resolve, a human rights advocacy group that tracks the LRA, said the US Government would lose credibility if it declared victory prematurely.
"This is a legacy issue for the Obama Administration," Ronan said.
"If we give up on this mission, it sends a message to the rest of the continent that if you outlast us for a few years, essentially we'll just give up."
To track down Kony, the US military and allied African forces are trying to navigate a territory the size of California with few roads and plenty of thick jungle terrain. But the biggest obstacle may be a wave of political turmoil that has further destabilised already weak countries.
Two US military camps are located in the Central African Republic, which is still embroiled in the sectarian civil war sparked by the Seleka rebels. Dozens have been killed this week in renewed clashes in the capital, Bangui, which has been seized by anarchy despite efforts by the United Nations and outside powers to restore calm.
Another US camp is in South Sudan, a country that declared independence four years ago with backing from Washington, but which has since become gripped by its own civil war. US military advisers are also posted at a small base in the Democratic Republic of Congo, yet another weak state wracked by warlords.
Kony has exploited the turmoil by moving from country to country and is now believed to have taken refuge in Sudan. US officials and analysts say Kony and LRA fighters operate primarily from the state of South Darfur and a disputed territory, Kafia Kingi, that is controlled by Sudan.
Sudan is a longtime antagonist of Washington, and US Special Operations forces are prohibited from entering the country. Instead, a small team of American advisers this year set up a new camp as close as possible, inside the Central African Republic, about 50km from the border with Kafia Kingi.
Although the camp is new, US forces have surveyed, selected and occasionally used landing zones in the area since 2013. The rudimentary base is near the town of Sam Ouandja, an area rife with smugglers and controlled by a local faction of the Seleka.
"When you do a map of who has power in the area, they're the ones. They have the guns," said Lisa Dougan, president of Invisible Children, an advocacy group that drew worldwide attention to the LRA's atrocities three years ago with a video - "Kony 2012" - that went viral on the Internet.
The Seleka and the LRA have a tumultuous history. Sometimes they engage in open warfare; other times they do business.
When the two sides aren't shooting at each other, LRA fighters often cross the border from Sudan into the Central African Republic to sell gemstones or elephant tusks in exchange for food and weapons, according to advocacy groups and U.S officials.
As a result, Seleka warlords have become as well-versed as anyone with the LRA. That, in turn, has led the US military advisers - despite Washington's distaste for the rebels - to work closely with the Seleka.
According to US military officials, the team of US troops in Sam Ouandja meets regularly with Seleka leaders, obtains intelligence from the rebels and sometimes provides medical care to Seleka loyalists.
"We're engaging with whomever has information that is relevant," said Amanda Dory, the deputy assistant secretary of defense for Africa. "Any time we have an intelligence lead that would help us locate the LRA or Kony, we pursue those leads the best we can."
The US military official who was critical of the cooperation said the Seleka was trying to win legitimacy by appearing to help the Americans look for Kony. But he suggested the Seleka couldn't be trusted and that the rebels were too cozy with the LRA.
"The LRA doesn't come into the area and attack or kidnap people," the official said.
"They come into the area to do business with the Seleka."
More often than not, potential leads on the LRA don't pan out, with US forces committing aircraft and personnel to far-flung searches that yield no results.
"Imagine searching for 200 criminals in an area the size of California covered in jungle," the military official said. "Between poachers, the ivory trade and the LRA, you don't know who's who."
