Could it be that the tranny just needs a flush? I'm surprised the dealer didn't try to sell you that.
Do check the engine mounts. It does sound like the CPU is having a brain fart but why only when cold? The life partner's Mini will sometimes do that, but it isn't temperature dependent. The software may have a sort of learning feature that makes adjustments depending on how you drive. Not sure if that is something that can be reset by disconnecting the battery for a time. May be a trip to the dealer, along with the new software.
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