Bob,
There doesn't seem to be anything untoward in the log information you sent.
To figure out why /home is empty, you should post the specific rsync_bpc commands (that are in the XferLOG file).
Note that for 4.1.2, I added --one-file-system to the default $Conf{RsyncArgs}, and it also adds that argument for 3.x upgrades. In 4.1.3, it's still in the default $Conf{RsyncArgs}, but it no longer adds to 3.x upgrades. This could explain why /home is empty.
Craig