So wife ran an update on the 3DS without thinking or asking me. Now now the Acekard won't boot.
There was a new update on the Acekard site but that doesn't do any good if the 3DS won't boot the card.
Luckily it still worked in the DSi as hardware updates don't get pushed to it. Yeah for keeping older hardware around.
Update the AKAIO software first. Then run the firmware update update for the AK2i card on the DSi. Then put it back into your 3DS and you should be good to go.