Whereas I am loathe to add anything to the always excellent instructions from Milhouse, as I recall it, the ability to boot from mmc(1) and mmc2 was fashioned by Fanoush in the event that you had chosen to install your cloned operating system on either of the cards, or both (as I once did with OpenBox Rox and KDE). Milhouse's instructions' default I believe would put the clone on MMC1, and that is the one to click on in the boot menu. If you have no clone on MMC2, it will revert to flash as you have experienced. I myself have edited the mmc2 option out of the boot menu when I reverted to only having one clone, and that on my mmc1.