The automatic transmission may develop shifting concerns. On lower mileage vehicles, upgrading the software in the powertrain control module (PCM) and the transmission control module (TCM) may correct the problem. As the mileage increases, internal transmission damage can occur. Repairs could involve replacement of the valve body or a complete transmission rebuild. Whenever major transmission repairs are made, it is important to be sure the PCM and the TCM have the latest software updates to help prevent these issues from reoccurring.
Car Problem Reports
Lincoln Zephyr Harsh or Delayed Shifting of Automatic Transmission
Lincoln Zephyr Problem
Model Year Affected: 2006
Average Mileage: 83,846 mi (55,000 mi - 130,000 mi)
Was told by a lincoln service shop the car needs a new Valve Body. They say the diagnostic report came back without any codes. Problem began with the LED panel on the instrument cluster working intermittently. Then I noticed it sometimes didn't shift smoothly. Finally, there are sometimes clunking noises, and sometimes a different noise when turning. Other times the car drives fine. The care went from having a clean bill of health at 84K to all these problems at 90K. All regular maintenance and oil changes have been done and the car is not driven hard. I understand this is a known problem with Ford/Lincoln transmissions.
Visitor, 2006 Lincoln Zephyr, 87,000 mi
Car will not accelerate when merging into interstate traffic, it hesitates and slowly adjusts. I am afraid a semi will not see me. I am told to see a transmission person. Is there this not a know defect?? I just had to spend $2100.00 to fix this. Frustrating
I have problem with my transmission slipping and shifting hard. Now the problems has gotten worse...started experiencing slippage while driving and hesitation in acceleration.......
Visitor, 2006 Lincoln Zephyr, 67,000 mi
Car skips when driving up hill/or needing to increase speed intermittently. Dealer states no code upon diagnois referred to DTC update. Recommend 'value body' repair and reset codes. Still working to solve problem
Visitor, 2006 Lincoln Zephyr, 83,000 mi
2006 Lincoln Zeypher in Columbus, Ohio. The car will not shift out of first gear, it will not excel over 20 mph. Right now it's sitting at a garage where they have quoted me $3000.00 to replace. It ther a recall on this transmission? Purased only 9 months ago in Mayfield Heights, Ohio from a large well advertised dealership. They offer no help. Anyone know a fair, honest transmission shop in Cleveland or Columbus?
Shifts hard when I step on it, also sometimes at lower speeds decelerating.
Visitor, 2006 Lincoln Zephyr, 130,000 mi
Noticed issue over a year ago. Have been told by a dozen mechanics it could be a dozen different things. Has been going for well over a year with this issue and no complete failure yet.
Visitor, 2006 Lincoln Zephyr, 55,000 mi
once in awhile at about 25-30 mph when i step harder on the gas to merge or change lanes the transmission shifts really hard scaring the heck out of me. I thought for sure something was broken. Took to the authorized Ford repair and they of course said there was nothing wrong. this has happened at least 6 - 10 times over 2 years, so far it is still drivable. I now have about 66,000 miles and hope i can sell it before it breaks.
Visitor, 2006 Lincoln Zephyr, 79,000 mi
noticed it after 24 hours of owning. we just try and baby the car.
Visitor, 2006 Lincoln Zephyr, 62,000 mi
Wouldn't shift into passing gear or shift while going up a hill, a knocking noise and a jerk would occur. Mechanic said the Main Controller (transmission) needed to be replaced. Just got it back from the shop yesterday and passed 8 people on the highway with no shifting problems :)