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DME should has different ZB Number for manual and auto. But as you installed R55 manual DME it already has this....
Better way surely would be to have left R56 setup, flash DME with winkfp 6MT and then VO code CAS and FRM by removing auto code and adding manual code with NCSExpert. Then default code all modules.
No matter what you must code DSC / ASC.
What interface are you using? I never touched a mini but I believe you'll need an ICOM for DSC / ASC for r56. That or maybe the new DCAN firmware like Bimmer Geeks cable but I'm not sure to be honest.
Also in case it helps, did you reset DME transmission stored values with INPA? Coding with NCS won't clear these necessarily.
Choose engine DME -> F5 (status analog/digital) -> F1 (digital values) -> F5 (vehicle options)
If auto trans still displayed, -> F8 clear DME stored values.
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