I met with the same issue in 16.04.1 (amd64). Tested several 'tar' archives 
(namely tar.7z and tar.gz) - none of them stored backup files. Maybe some 
problem with generation of the lists of files for archiving? '7z' and 'zip' 
archives do save backup files, but it seems that they rely on 'p7zip-full' 
package which provides 7-Zip backend for the File Roller. Until I installed 
this package 'zip' archives were also losing backup files.
In my older system which is 12.04LTS (i386) all the mentioned archive types 
properly store backup files.

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https://bugs.launchpad.net/bugs/1571806

Title:
  Backup files are silently ignored when using certain archive types

Status in file-roller package in Ubuntu:
  Confirmed

Bug description:
  Depending on the kind of archive you create using file-roller, backup
  files (files with a `~` on the end of their names) are included or
  ignored. The user doesn't see any warning at all and will probably
  only discover this when they try to extract the archive.

  # How to reproduce the symptom.
  (I'm assuming you're using Nautilus with file-roller integration.)
  Create a folder `testFolder` (or any name but I'll use this one to refer to 
it) and create a file called `testFile~` in it. Then move to the parent folder 
of `testFolder`. Right-click test folder and choose "Compress".
  ## Correct behavior.
  Choose `.7z` as the archive format making it a 7zip archive and click 
"Create". The archive will contain the folder `testFolder` and in it the file 
`testFile~`.
  ## Incorrect behavior.
  Choose `.tar` as the archive format making it a tarball and click "Create". 
The tarball will contain the folder `testFolder` but it will be empty.

  Note that this isn't the fault of `tar`. If you create the tarball
  from the command line using the command `tar`, `testFile~` will be
  included.

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