Try to use a regular DS dumper, because the bootstrap does not seem to need the DSi specific region to work...
On my Cyclo Ievo I used the french version of "My Cooking Coach" (which is needed to create the euro bootstrap), it worked but when I tried the game on the Ievo it said that it doesn't have the DSi specific section of the rom.
And the DSi mode actually works perfectly for every other games/homebrew.