Hello,
Thank you for making a bug report.
I believe that this is for one of 2 reasons. 1 is because you are playing against the AI. I do not believe the AI is capable of having a double deck qualifying deck, thus it’s pairing your down to 40. And 2, because you are playing local. The local system isn’t 100% at this point in time.
I believe online, with a human opponent, you should be able to use Double Deck successfully.
Please let us know if this is not the case.