Sounds like it's a hardware update. It's possible that in order to meet demand, some of the DSi coming out in certain places are utilizing the old hardware with a different firmware for specific regions. As the stock runs out of the older hardware, the newer revisions with the protection built in will take their place.
This happens on the PSP scene a lot with different batch of motherboards being produced to try to curve piracy.
This happens on the PSP scene a lot with different batch of motherboards being produced to try to curve piracy.