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I have a 2006 M5 and last night I got the error transmission malfunction and now when I start off in first gear the whole front of the car shakes. This only happens when I am at a stop and start to move forward after that everything seems to run fine.

Anyone have any idea what might be causing this is it the SMG pump failure? I have a after market warranty that says all lubricated parts inside the transmission are covered hopefully falls in that category.
 

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Sounds like the clutch or a throwout bearing problem. Take it to the dealer and have the codes pulled, once you have them post in in your thread so members on the board can comment on the specific failures. It could be the SMG pump, however it would affect shifting in all gears not just at take off.
 

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Here are the error codes 4fa0/ 4f82/ 4f80. The dealership says it the clutch and flywheel which the clutch is not covered by warranty. Trying to get the warranty to replace the flywheel since it says on my paper it is covered.
 

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First off, look above at the thread regarding cheapest clutch. The run away from the dealership. On a flatbed if you have to.

according to ISTA,

4fA0 clutch (activation position deviation)
4f80 generic smg gearbox error
4f82 engage 1/R gear not possible

I recommend finding an indy repair shop and having them do the SMG gear position teach-in, clutch teach-in, and clutch slip-point setting in either DIS or ISTA/D. There are a number of diagnostic tests associated with this that will determine if any of the gear actuation solenoids are not repositioning correctly.

I was getting a daily 4FA0 and a 20 second red cog. The car was horrible going from neutral to 1st, and kicked you in the back of the head until you reached 4th.

I had the dealership do the SMG adaptations (supposedly) and did not see any difference. I used ISTA myself yesterday and for the first time in the two months I've owned my car I thought it finally shifted better than my SMG M3.

If those things don't work or at least help, it could be the clutch and flywheel. But, I'm a firm believer in not taking things apart just to "easter egg" for an answer. While chasing those exact error codes in ISTA, one of the steps in their diagnostic procedure tells them to drop the gearbox for inspection. Not to replace things, but to look at it.

I get it for a car under warranty, but from the point of view of a customer who will be paying for a clutch (I think the days of warrantied clutch replacements are about gone if there were many to start with), perhaps trying the recalibrate the transmission first and let them drive it for a while makes sense. At least give them the option. But let me guess, they're going to charge you $2500 in parts for the clutch and flywheel, probably won't think to spend the other $85 in parts that make sense to make all the mechanicals like new and will still charge you for 16 hours of labor at some ridiculous rate.

A local indy quoted me $800 for labor to do the job and a clutch and flywheel from Bimmerzone is $1499 shipped.

It could be the clutch, but I'm amazed how quickly the dealers jump to say replace it when there is no indication according to their own diagnostic procedure telling them to.

Ask them to do all three steps of the SMG functions and ask to watch while they do it. If they won't let you, ask for your keys or a flatbed.
 
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