You need to have all the proper settings in config.ini.php
If you're using 'config' as your 'auth_type', then you should have:
$cfg['Servers'][$i]['controluser'] = '';
$cfg['Servers'][$i]['controlpass'] = '';
$cfg['Servers'][$i]['auth_type'] = 'config';
$cfg['Servers'][$i]['user'] = 'super_user;
$cfg['Servers'][$i]['password'] = 'your_pass';
$cfg['Servers'][$i]['only_db'] = '';
If you're using 'cookie' or 'http' or 'advanced', you need ot have:
$cfg['Servers'][$i]['controluser'] = 'super_user';
$cfg['Servers'][$i]['controlpass'] = 'your_pass';
$cfg['Servers'][$i]['auth_type'] = 'cookie';
$cfg['Servers'][$i]['user'] = '';
$cfg['Servers'][$i]['password'] = '';
$cfg['Servers'][$i]['only_db'] = '';
Right now, you're probably entering as a normal user if you're settings aren't properly configured. While you logon as a different user from the console.
Another thing to check is if you have in your 'user' table of the 'mysql' database 2 same users with different passwords/access rights?
Also make sure that you're using the latest version (at least 2.3)
Let me know!
.M