Select "Write MBR" from the Boot menu or use the make-bootable script to write the magic strings to the MBR of the CF card:
offset 0x47: EOS_DEVELOP offset 0x5C: BOOTDISK
Additionally the DISKBOOT flag must be set to enable to firmware boot loader to check the status of a bootable card. Select "Autoboot ON" from the Boot menu to enable it or disable it when it is not desired to auto-boot Magic Lantern.
The AUTOEXEC.BIN file must be present on any card marked as bootable or the camera will hang on bootup. This is a raw ARM binary that will be loaded at 0x800000 and there is no header, nor any checksum. The reboot.bin shim has been updated to deal with the different offset and can now be used without any changes to allow Magic Lantern to automatically boot.
Card Tricks (from CHDK) utility bootable.exe write these strings to another offset (0x40, 0x2b, works with FAT16 only) don't use it for FAT32.
A modified version of this tool (works with FAT32 cards) available here: bootCF.exe (Win, 9kB).