Craig released BackupPC 3.3.0 earlier this year. This version adds a number of fixes, including a minor one from yours truly. It also fixes the issue with Samba 3.6.x.
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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.
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