How do you know it's not charging? Has the battery been tested and connections checked?
I'm surprised that the alternator shop wouldn't diagnose the problem? Of course you would have to pay if it turned out to be something other than the alternator.

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1988 325is (purchased new) sold
2004 X5 3.0 2005 X3 2.5
2008 X5 3.0 (new to me)