Is it a warning from the DS or from the flashcart?
Did you use the latest version of R4 Wood for the R4i Gold?
It most likely is a problem with your boot loader not working with the latest 3DS firmware.
Most R4i 3DS carts work out of the box, but apparently there are some the don't, which is why the R4ids.cn team released a fix.
I hope you have a DS Lite/Phat or DSi that still works with the flashcart.
Because you will need this to update your boot loader for the cart to work with the latest 3DS firmware.
Download the boot loader update here:
Put the nds file on your micro sd card and run the flashcart with a DS that works as mentioned earlier.
Now run the update and follow the instructions on the screen and you should be ready to go.