Hey my friend (and anyone else that is eavesdropping) - there is a candidate for a new release (0.5d) which incorporates a couple new features, not the least of which is the patch for an authenticated site like yours. It also supports multiple connections.
I took the time to really comment in the config.php file exactly what each variable should look like. What I was hoping is that you'd DL the new one, look through the README, INSTALL and config.php and see if it all makes sense... then of course, that it works right out the box as it should. I'd like to get it happy with your database and then release it this week if possible.
I've attached it here so you can grab it, or you can get it via the main website here:http://www.phpmyide.com/images/phpMyIDE-0.5d.tar.gz
Please let me know what happens. If you get it running satisfactorily I'll post here how to use multiple connections.