That implies a very corrupted eMMC to me -- since a normal SD card
flasher does not turn the eMMC into a "flash" mode.
We're out of my diagnostic experience -- I'd probably try using a
standard images from http://beagleboard.org/latest-images, editing the
u-Boot script to define it as a flasher (may not matter if your eMMC is
already trying to copy from the SD card), and flashing with that image.
Since normally the "flasher mode" text does not get copied to the eMMC (or
is post-flash modified).
If that didn't work -- I'd have see if JTAG is capable of erasing the
eMMC, and purchase a JTAG unit.