Until now, the firmware loading mechanism (loading the diskboot.bin from a locked card with the BOOTDISK signature at offset 40h) did only work with FAT12/FAT16 fs format.
Maybe Canon has changed this, you could test it easily:
- format the 4GB card in the camera, this way the Canon fw creates one partition, FAT32 formatted
- write the BOOTDISK
signature to the card, e.g. with CardTricks 1.45 or with a hex editor (hxd
- copy your diskboot.bin to the card, lock the card
With the old behavior you'll get a "card locked" message, otherwise CHDK should start...