did you flash the eMMC from the SD card? That'd be this step.
If you already did that, try again, but yes, we may have a problem. I think I had one BBB (out of a few hundreds I handled myself) where the eMMC was not working as expected: it would seem to be fine if you flashed it, but then on reboot it failed. Maybe this is a similar issue? After all, your initial failure was probably linked to an eMMC corruption ... maybe it has failed completely?