Your problem seems to me like a result from a bad copy to eMMC.
You have just dubbed the (already running) SD card I guess, this wont work, because each card gets a different ID. Therefor the mount on the next boot from eMMC will fail.
What you need to do is to use the orginal image (that one that does autoexpand on the first powerup) and flash it onto the eMMC ON A DIFFERENT Computer! Do not run the image yet, just copy it with a PC or something. You may need that cheap eMMC->SD adapter board for this.
After the copy insert the eMMC, fire up the Rock, let the filesystems expand (and create a unique ID and mountpoint).
(This only needs to be done ONCE for the initial install. Updates afterwards can be installed the usual way and wont harm that config anymore)