Thanks all for your comments. I think I remember reading about the broken wire but had not checked it yet. I have just removed the rubber conduit and I cannot see any broken wires but of course they could be broken internally.
I do have permanent 12v at the amplifier though so that one is OK. The one that runs to the GM3 I am going to run a temporary wire between the two to rule that out, wont get a chance for a few days though.

I've recently noticed that I have to warning tone if I open the drivers door with the key in the ignition. Could this cause an issue with syncing the key?

To answer other replies, I have two remote keys.

I have scanned and only 3 or 4 keys have been registered.

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2006 X5 3.0D Auto RHD