I have no problem booting from the mmc with ext3 (different partition too).

only thing you need is change the bootmenu.sh in the fanoush's initfs_flasher dir before flashing the menu. Make no mistakes though

For instance booting ext3 from partition 2:

MENU_3_NAME="MMC card, partition 2, ext3"
MENU_3_ID="mmc2"
MENU_3_DEVICE="mmcblk0p2"
MENU_3_MODULES="mbcache jbd ext3"
MENU_3_FSTYPE="ext3"
MENU_3_FSOPTIONS="noatime,data=writeback"

if you want to boot from partition 3 - you need to change the device to mmcblk0p3.

If you make a mistake - boot from flash and reflash with the correct menu. If you made a bigger mistake (i don't know if the device will continue to boot if bootmenu.sh has incorrect syntax), use the fanoush's flasher bootmenu image to put on the correct menu