If you previously used the app to install Flipnote Studio or other exploits, your SD card may contain a folder called HBFILES .
By systematically checking your SD card format, your folder structure, and removing the HBFILES folder, you will resolve the error in 99% of cases. If all else fails, booting boot.nds directly through the Unlaunch file menu will force a repair installation. twilight menu dsi binaries missing install