Because of the command you provided I've been able to see that the second disk has not been used yet. All files so far have been put on the first hd.
I thought the empeg was supposed to balance the files across the two drives adding them to whichever had more available space? If that is true you should have files on the 10Gig drive at this point. Maybe the files that are disapearing are the ones that should be going to the 10Gig? If that is true it might explain why it worked fine for the first 13 hours, that was how long it took to fill the larger drive to the point that they both had the same amount of free space.
So maybe the empeg can't write to the smaller drive for some reason. Have you verified that after a rwm you can create a file by hand on the smaller drive?
-Mike