The default rsync arguments in v4 include --one-file-system, which could be
why it's not descending into those directories (ie, are the missing
directories different file systems?).
If so, you can either remove --one-file-system (in which case you'll need
to explicitly exclude things like /proc),
I've made quite a bit of headway on my issues deploying a BackupPC 4
server. I was having issues with the $Conf{RsyncClientPath} because the
client path on FreeBSD is /usr/local/bin/rsync, whereas on Linux, the path
os /usr/bin/rsync, and specifying it in the per-host config files did not
override
Per-host config files are working fine for me. Maybe your
RsyncClientCmd has the rsync path hardcoded in it instead of referencing
$rsyncPath?
My environment is mostly-linux with a few BSD-based hosts and, to just
pick a .pl that contains "local" at random-ish, I have: