Update 2013-10-02: This issue has been resolved with BackupPC 3.3.0.
A number of people of reported issues backing up Windows hosts with SMB and BackupPC 3.2.1 on Ubuntu 12.04 precise. This is caused by a bug in Samba/smbclient since 3.6.x where excluded directories are still listed (even if they won’t be backed up). It has not yet been fixed, but there is a workaround: downgrade Samba to 3.5.x.
You can now work around this problem by adding my repository to your BackupPC server and running:
sudo apt-get update
sudo apt-get install smbclient=2:3.5.11~dfsg-1ubuntu2.3 samba-common=2:3.5.11~dfsg-1ubuntu2.3 samba=2:3.5.11~dfsg-1ubuntu2.3 libwbclient0=2:3.5.11~dfsg-1ubuntu2.3 samba-common-bin=2:3.5.11~dfsg-1ubuntu2.3
echo "smbclient hold" | sudo dpkg --set-selections
This will downgrade smbclient and its dependencies, and mark them held so APT won’t attempt to upgrade them.
The following Samba packages have been added to the precise repository, all version 3.5.11~dfsg-1ubuntu2.3, for amd64 and i386.
Thanks to Mike Lerley for reporting this issue and helping test the workaround.