I had this problem and this is how I solved it. Maybe it can help others. I received this warning after upgrading to version 2.50 today (I did not have this warning before):
"Your backup folder MIGHT be visible to the public
To correct this issue, move the .htaccess file from wp-content/plugins/wp-dbmanager to /home/username/commondork.com/wp-content/backup-db"
I didn't have an .htaccess file in /wp-content/plugins/wp-dbmanager. So I created one in the backup-db directory using the information from this post http://forums.lesterchan.net/index.php/topic,1489.0.html
The easiest way to do this is to copy the code provided by the link above into a file named htaccess.txt then transfer that file to your backup-db directory. Once it has been uploaded simply change the name of the file from htaccess.txt to just .htaccess. Browse to your backup-db directory and you should see a 404 error now instead of a directory indexing.
I hope this helps anyone having a similar issue.