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What's really going on with the 2014 Jeep Cherokee's transmission issues?

On September 23, Automotive News reported that Chrysler had idled the second shift workers it hired just five weeks prior at its Toledo Assembly Complex to build the 2014 Jeep Cherokee. At the time, Chrysler said it had "built the critical number of vehicles we need to stock dealerships once containment is released" and did not want "to put additional strain on our logistics partners ... upon release." That reasoning was not only unusual, it didn't seem to make sense.
It appears the center of the nine-speed issue is software, not hardware.
That same day, the Detroit News ran a piece claiming workers at the Toledo factory said the halt was due to issues with the Cherokee's transmission. It put the number of already-built Cherokees needing fixes at 1,000 and said that some of the workers not laid off had been instructed "to take the Jeep on long test-drives." That made more sense. Three days later, on September 26, Automotive News reported that the 500 workers laid off had been reinstated, with engineers "speeding repairs on the SUV's powertrain software." The AN piece didn't put a number on how many units are being fixed, but it did say that 12,000 have been built and are awaiting delivery to dealers. The best it could say about when dealers will get them, however, is that "progress on a fix is being made. It's unclear when shipments to dealers will start."

Consumer Reports says these are the worst new cars of 2014

Consumer Reports has announced its annual list of worst vehicles, a cringe-inducing contrast to its list of top vehicles. Ignominiously leading the way in 2014 is Chrysler, which has a staggering seven models listed.
Jeep nearly sweeps the small SUV segment by itself, with its Compass, Patriot and 2.4-liter version of the new Cherokee, while the only midsize sedans listed by CR were the Chrysler 200 and Dodge Avenger. The new Dodge Dart and the Dodge Journey round out CR's condemnation of Chrysler.
Ford is taking heat as well, with the Taurus, Edge and their counterparts from Lincoln all listed as the worst vehicles in their respective segments. Toyota doesn't fare much better, with its Lexus IS, Scion iQ and tC also making the list.

AEV Jeep Wrangler Unlimited Rubicon

After their rented 2007 Hummer H3 failed them during the brutal Rallye Aicha des Gazelles in Morocco, Amy Lerner and her sister Tricia Reina were on a quest to find the most capable production off-roader for their next competition - they chose a 2012 Jeep Wrangler Unlimited Rubicon. Their next mission was to find a company with the competence to configure it to win. After poring over Internet forums and perusing countless magazines for an outfitter who could meet their demanding requirements, they sent their bright orange JK ("Crush" is the official color) to American Expedition Vehicles (AEV) for some modifications.
The Michigan-based team at AEV kept the Jeep's 3.6-liter V6 and automatic transmission stock, but replaced the hood with a tall AEV Heat Reduction Hood and added an AEV Snorkel Kit for water crossings (it serves double-duty as its raised height helps to keep the air intake out of the kicked-up dust on the trail). Front and rear off-road bumpers were bolted in place, and AEV skid plates were added to provide additional undercarriage protection. A pair of IPF-900 off-road lights improve visibility, while a 10.2-gallon AEV Fuel Caddy (located behind the exterior spare) added some range. The suspension was upgraded with a 3.5-inch lift kit with Bilstein remote reservoir shocks, and 35-inch Falken Wildpeak A/T tires (LT285/70R17) were mounted at all four corners on AEV's beadlock wheels.