So more to the story and some false assumptions. Obviously both keys were not emitting like you said, and you failed to mention you replaced the battery, probably with a wrong one. Maybe switch the order of the keys when you synch them and see what happens then.

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