I only have one box myself, so I never had to go throug that 'pairing' method myself, but I believe one simple error to make is to forget turning the other box off when doing the pairing of one remote to the box it should control.
I'd try doing that procedure over again, for both remote+box pairs, until both boxes respond properly to the remote it is 'paired' with, including shutdown ability of course. And if that seems impossible to achieve I'd seek more detailed help with it here again.
Best regards: Ronald



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