DMA should be enabled by default for most games, and should only be disabled, if there's issues with wireless.Had the same error with the clean ROM, but setting it to DSi-mode and deactivating DMA did the trick.
There's a flag in the ROMs header that says it's DSi-Enhanced or Exclusive.Btw. how does Twilight work with DSi enhanced games? Does it detect that automatically or do I have to enable it for every enhanced game separately? I saw there's an option for Audio in the general bootstrap settings, but not for DSi mode.
In nds-bootstrap, additional patches are applied for the ROM to run in DSi mode.