New day new problem
Yesterday i started my car normally, had to make a stop, turned off the engine.Came back, gave the contact and immobilizer started blinking.Tried on and off contact for several times and it won't go away.Finally i disconnect the negative line from the battery, leave it for 2 minutes, put it back on and the immobilizer light goes away and I was able to start the car.
Finish my drive, turn of the engine, and gave contact again just to see if the problem would pop out againg.And there it was, blinking again.Same thing today.
Let's me start the car the only after the I disconnect the battery, wait for a minute or two(if i connect it immediately it wouldn't resolve the issue) and gives me one chance to start the car.For every stop, every other contact I give to the car i need to obviously disconnect the battery, maybe the computer resets this way i dunno.
I must mention that i don't have the second key, only one original of course.

What could be the issue, is there something I can do to resolve this, some elementary troubleshooting.

 

You need VAG COM.

 

Haven't had the time until today so I called this repair guy to make an appointment, I explained the symptoms and he told me that diagnostic would only show the immo error and that can mean practically anything from faulty ECU, immo itself, the transmitter in the key, bad wiring...bunch of things.
He basically told me that diagnostics won't really help that much, so I don't know what to think? This guy was recommended to me, should I call someone else?

 

That's bullshit. My nephew recently got a great deal on a B6 because the owner couldn't figure out why the car kept shutting off and why the lights kept blinking. His car had the same exact problem as yours (from what you're telling me). I got in there with VAG COM and disabled the immobilizer (for testing purposes) and it fixed the problem immediately. I then reprogrammed his "comfort system" (or whatever the B6 version of the CLS is) and keys and he was good to go.

It sounds like your mechanic understands diagnostics, but doesn't understand the capabilities of VAG COM (which is typically the case with non-German specific mechanics).

IE: OBD II basically does what he says. It shoots out codes and nothing else. You then reference the codes and go form there. VAG COM does that as well, but it also has the capability to go in and fix problems like yours. It's an interactive program. Not just a diagnostic tool.

G/L

 

ok thanks alot, I'll keep updating

 

The finale of the story, I ended up doing immo off, basically a chip from the ECU is removed, reprogrammed i placed back on the ECU.That way immobilizer is bypassed on the ECU.Cost of this modification was little less than 30 euros.
After being presented with all the options this was like the cheapest and painless method to solve immo problem, diagnosing the problem step by step and solving it would cost a lot more and take more time since there is so many things that could cause immo errors, like the key itself, immobilizer, cluster, ECU going bad, bad wiring and installations.

 

Glad to hear you got it dealt with.