Common restrictions
Deduplication cannot be performed if you protected the archive with a password. Data blocks of password-protected archives are stored in the backups as they would be in a non-deduplicating vault.
If you want to protect an archive while still allowing it to be deduplicated, leave the archive non-password-protected and encrypt the deduplicating vault itself with a password. You can do this when creating the vault.
Disk-level backup
Deduplication of disk blocks is not performed if the volume's allocation unit size—also known as cluster size or block size—is not divisible by 4 KB.
Tip: The allocation unit size on most NTFS and ext3 volumes is 4 KB. This allows for block-level deduplication. Other examples of allocation unit sizes allowing for block-level deduplication include 8 KB, 16 KB, and 64 KB.
File-level backup
Deduplication of a file is not performed if the file is encrypted and the In archives, store encrypted files in decrypted state check box in the backup options is cleared (it is cleared by default).
Deduplication and NTFS data streams
In the NTFS file system, a file may have one or more additional sets of data associated with it—often called alternate data streams.
When such file is backed up, so are all its alternate data streams. However, these streams are never deduplicated—even when the file itself is.