According to long running GBA and DS homebrew site GBATemp, The DSi, Nintendo's update to the DS Lite, blocks almost all current flash carts from running code on the system. That includes the infamous R4, CycloDS and M3 cards.
Right now, there's no telling if this can be fixed by updating the card firmware, or if people who want to run code on their DS (homebrew and pirated ROMs alike) will simply have to wait for the next generation of flash cards to spew out from the factories of Hong Kong. Which they will.
For me at least, this is just another reason not to pick up the DSi (besides the fact that it has noticably worse battery life than its predecessor). I won't pretend to find the homebrew scene on the DS very compelling (as opposed to the PSP, which has a number of great source ports and emulators available that I really enjoy) but I also find the convenience of carrying all of my purchased games on a single cart invaluable. If Nintendo can offer up their own storage solution for doing just that, fine! Let me at it. I'm happy to exchange solutions. But carrying around a half dozen postage stamp sized carts with me every time I board a plane or a train is something I haven't had to do for a couple years, and I'm damn well not going back.