I have the same issue.
After upgrading to Sierra, I encountered to very slow backing up at the first time, but it was still working (generating a backup).
Eventually it started not working at "preparing...," though.
I initialized the backup HDD and tried baking up.
The initial back up was done very smoothly and some of the following differential backups too.
However It started failing again at a new differential back up.
I repeated such (initializing the HDD, baking up from a scratch, making hourly differential backups, etc.) several times.
Eventually the process fails.
This morning I found a file named 2016-09-25-001350.inProgress in the backup HDD and I moved it to Trash (the file cannot be erased, though).
Since then the differential backup has been working several times.
I have to see if this has fixed the problem or not for some more time.
I feel that the above backup failure at a new differential backup started once the "initial encryption" was completed.
After the initial backup, the encryption started and went well. New differential backups were made smoothly during that encrypting. However suddenly after the (deemed) completion of encryption it appears to fail a new backing up.
I am not sure if the encryption is a cause of this trouble and if the encryption was truly completed.
I can look into and manipulate all of the folders/files in the backup HDD by Finder. Is this normal?