I got an M3.
The Quake homebrew didn't work on my M3. :(
Try harder, it took me several tries to get it to work but it finally did. :D
Did you remember to patch the quake.nds file? I'm pretty sure you need to do that for R4s and M3s.
Are all the files in the right places? ex: the pak file/s are in a folder named ID1 in the root of your SD card?
Also, you may have to hold L while it is starting up (thats what I have to do).
Warning:
Because the DSi has the current DS flashcards blocked, most of the original flashcarts wont work on the DSi
You can get DSi compatible flashcarts, ex: Acekard 2i, EZ-Flash Vi.