pt-table-checksum toolkit for few databases from file
I would use a 'for' loop for this, which I have found easier to use for things like this. Often, either line break, spaces, or combinations of those can cause issues with your method.
Also, remove the --quiet from your command line to see the errors that pt-table-checksum may be reporting.

#!/bin/bash

for db in `cat /etc/backup.conf | egrep -v "(^#.*|^$|^--.*)"`
do
    pt-table-checksum [options] --databases $db --quiet
done


(Hope this reads ok, have answered on my phone!)