If I am reading this correctly. Your DSi functions correctly except when you put your r4i card in the slot. You will need to go to the support web site for your r4i card to see if there is an update for it's firmware to get around your DSi's new firmware. Follow their instructions there for how to update the card, if one is available.
If there isn't new firmware for your r4i card to get around the DSi's new firmware, you will need to wait for them to put one out or buy another media card that works with the DSi firmware. Until then you can enjoy the games you have paid for.