[eluser]Randy Casburn[/eluser]
Right...that's because I was wrong. Sorry.
Bad news. I looked at the code for the DB utils class and it reads your database.php default_group setting out of the config file and completely ignores any loaded databases. Therefore, you cannot backup any database that is not currently set as the default_group in the database.php config file.
The relevant code is on line 40 of DB_utils.php which makes reference to $CI->db that is set between lines 32 & 47 of DB.php.
I recommend you create your own work around or recommend a change to the core. They will take this up if it makes a difference to the community.
I will tell you from experience that multiple database issues don't get a lot of visibility. I'm not sure why. Most likely few of us are actually stressing that test I suppose.
Sorry for the bad news.
Randy