E38 O/S compatibility issue

Hi there,
I had a look on the forum and I found that E38 2010+ 12639270 and 12656198 were in the same column of the O/S compatibility PDF and should be compatible...however when I do a test full flash just to check things it comes up with a warning saying that they ARE NOT compatible and a tick box saying flash it anyways.
Maybe its because one is an Auto file and one is a manual file ??
ECU was in an Auto trans vehicle and is being transplanted into a Lambo kit car project with a manual trans.

Cheers,
Mike

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