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E39 540i Water-cooled alternator issues

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A few weeks ago, I got in my car and turned the key and ...nothing....just a click and a "boing" signal I have never heard. It was obviously flat bettery, but I was certain I had not left anything on. Anyway, charged the battery, and the car started fine, only to realise that the battery light was flickering on and off. Did some voltage tests across battery and using OBC test 9 and readings were all over the place, as well as noticing a pulsating of the dash lights when at 2-3k rpm. I bought a new battery, as my one was getting on 7 years, although it tested ok, which made no difference, but at least I knew the battery was now ok.

I concluded it must be a bad regulator, so popped the alternator out and sent it off to Jimmy at Advanced Auto Electrical in Strand, who had worked on this same alternator before, when the bearings went. There are apparently only a few people who know how to work on these water-cooled alternators, and Jimmy is one of them.

Anyway, it took a week for him to source the right regulator, fitted and returned the alternator. I popped it back in, only to turn the key and realise that now the battery light is on permanently, and that the alternator is not charging at all. Needless to say I was G-utted!

My car was due to go into Garage 808 the next day, so I decided to call Colin and tell him about what had happened, and we decided I should drive the car down to him, so they can take a look, while doing the work the car was booked in for. Apprehensively, I drove the car the 15 km to Colin's, and made it there no problem (Only battery charge) and the battery was not even fully charged.

The next day, Colin ran some diagnostics on the alternator and on the car. Meanwhile I phoned Jimmy and chatted to him. Of course, I wanted to know whether he had tested the alternator before releasing it, and then learned that this was not possible without the car, as this alternator required a data signal from the ECU, in order to work. And that the best bet was to drive the car through to Strand, so they can diagnose the fault. Meanwile, Colin was doing his tests and along with some other auto electrical guys he knows down the road, concluded that the alternator is at fault, and the car is fine, exept that they come to the conclusion that this car is not one that sends out a data signal to the alternator, and that the alternator is a basic one.

We then thought that perhaps Jimmy fitted the wrong regulator. One that had the data module on it, when it was not needed.

But I have checked RealOEM and the Bently Service manual and compared it to my alternator, and there is just 1 type of water-cooled alternator for this car, and it is the one requiring the data signal. I asked Colin about the tests they ran on the car, and they are convinced that there is no fault on the car's side, yet they can't measure a "pulse" signal, concluding a basic setup, when it MUST be a data signal setup, as per the part and the service book...

I am hoping that perhaps they measured incorrectly, because this might spell an issue on the ECU side? I am taking the car in to Jimmy's tomorrow, for him to take a look...

Anyone had any experience with these alternators...? Opinions welcome.

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