Neither machine has been improperly shut down since all this started. Both servers are running on a UPS, so I know there haven't been any power issues (checked the log on my desktop). I have shut the unraid box down a couple times, but that was always a proper shutdown through the web UI, and never while it was copying or syncing.
Actually, I still do have all the original files on the old WHS. I've been too nervous to delete them until I figure out what the cause of the problem is on the new unraid server.
Ran a long smart scan on all three disks, and all came up clean. Ran a non-repair scan twice, both times coming up with the same 11 errors. All 11 errors coincide with errors that the first repair scan "fixed". The original repair scan actually found 12 errors, so I guess the one error that hasn't popped up in subsequent scans was legitimate.
This stinks. As far as I can tell, nothing is broken enough to be obvious. I think my next step will be to switch around some of the SATA cables, just to see if that makes a difference.
EDIT: Rather than just swap cables, I swapped the trays into another cage that is running through the SASLP-MV8, re-assigned the drives to the correct slots and started yet another non-repair sync. This should rule out the MB SATA ports, the cables, and the backplane. If this comes up with the same 11 errors, I'm just going to fix them, move on with migration, and hope for the best. There's not much else I can do.