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What are the user groups on the database?
That would be SELECT user_id,user_name,ug_group FROM user LEFT JOIN user_groups ON user_id=ug_user;

From your output it seems like they're given emailconfirmed status, but it's not applied.

The name of the groups being in red is not relevant. You just don't have a page on the wiki talking about them.

I am not experienced in which manner MW stores which status information. The result of your proposed action is following:

=================
[root@mail ~]# mysql -u root -p mysql
Enter password:  ****

mysql> SELECT user_id,user_name,ug_group FROM user LEFT JOIN user_groups ON user_id=ug_user;
ERROR 1146 (42S02): Table 'mysql.user_groups' doesn't exist
mysql> 
=================

I have mapped the wiki, which's setup is described in the attachment, here:
http://www.axonnet.eu:8000/test/index.php/Main_Page 

This is not a production system at all thus you may try whatever you wish. This is a very simple installation made from the Mediawiki installation files only. However I shall have to switch this computer off later in the night (say around 22:00). Now it is 18:09 hours here in Prague. I shall check emails more often. I am also available on Skype account "axonnet.eu". Regards, Huck.

Hoops, wrong MySQL user above, I guess. Test1 created before changes of LocalSettings.php, Test2 after.
=========
[root@mail ~]# mysql -u testuser -p testdb

mysql> SELECT user_id,user_name,ug_group FROM user LEFT JOIN user_groups ON user_id=ug_user;
+---------+-----------+------------+
| user_id | user_name | ug_group   |
+---------+-----------+------------+
|       2 | Test1     | NULL       |
|       3 | Test2     | NULL       |
|       1 | WikiSysop | bureaucrat |
|       1 | WikiSysop | sysop      |
+---------+-----------+------------+
4 rows in set (0.00 sec)
=========

mysql> SELECT user_name, user_email_authenticated FROM user;
+-----------+--------------------------+
| user_name | user_email_authenticated |
+-----------+--------------------------+
| WikiSysop | NULL                     |
| Test1     | 20081101124829           |
| Test2     | 20081101130257           |
+-----------+--------------------------+

It's explained in the RELEASE_NOTES:

Configuration changes in 1.13:
* Removed the emailconfirmed implicit group by default. To re-add it, use:
$wgAutopromote['emailconfirmed'] = APCOND_EMAILCONFIRMED;

I have read RELEASE_NOTES of both 1.13 and 1.12 and I tried even this line within LocalSettings.php without success at some stage of my elaboration last week.

However, now it seems that it works as desirable, at least in this version of the installation.

=========Part of LocalSettings.php=========================
# HF: added according to the advice (since MW 1.13)
$wgAutopromote['emailconfirmed'] = APCOND_EMAILCONFIRMED;

# HF: Do not show pages to anonymous users (only to emailconfirmed)
$wgGroupPermissions['*']['read'] = false;
$wgGroupPermissions['user' ]['read'] = false;
$wgGroupPermissions['autoconfirmed' ]['read'] = false;
$wgGroupPermissions['emailconfirmed' ]['read'] = true;

# HF: Except of following "white" pages listed, use UTF-8 code to include national alphabets
$wgWhitelistRead = array(":Main Page", "Special:UserLogin", "Special:UserLogout", "Special:Preferences", "Special:ConfirmEmail");
==========End of LocalSettings.php citation=================

I would suggest to append this kind of LocalSettings.php configuration into one or more of the following manual pages:
http://www.mediawiki.org/wiki/Manual:User_rights_management
http://www.mediawiki.org/wiki/Manual:Preventing_access
http://www.mediawiki.org/wiki/Manual:$wgGroupPermissions

I have read even this section
http://www.mediawiki.org/wiki/Manual:User_rights_management#Automatically_promote_users
which claims: "By default, there is a group "autoconfirmed" and another one "emailconfirmed". Thus I supposed there is no reason to explore $wgAutopromote option more heavily.

User profile
Username:	Test2
User ID:	3
Member of groups:	Autoconfirmed users, Users, emailconfirmed {no hyperlink}

When I go over
http://172.20.20.49/test/index.php/Special:ListGroupRights
to
http://172.20.20.49/test/index.php?title=Special:ListUsers&group=emailconfirmed
it shows me users.

Thus I would conclude that "emailconfirmed" is a "virtual" group only, is it not? Regards. 

> I would suggest to append this kind of LocalSettings.php configuration into one
> or more of the following manual pages:
> http://www.mediawiki.org/wiki/Manual:Preventing_access
There's already a note on http://www.mediawiki.org/wiki/Manual:Preventing_access#1.10_upwards

> http://www.mediawiki.org/wiki/Manual:$wgGroupPermissions
It already states 'This group has been removed by default in 1.13.0'

> I have read even this section
> http://www.mediawiki.org/wiki/Manual:User_rights_management#Automatically_promote_users
> which claims: "By default, there is a group "autoconfirmed" and another one
> "emailconfirmed". Thus I supposed there is no reason to explore $wgAutopromote
> option more heavily.
Corrected.

1st. Now I may confirm that it works well even for the database after the upgrade.

2nd. I stil think it is underdocumented. When upgrading from MW 1.11 to MW 1.13.2 (cs - Czech version) I have to make two changes in LocalSettings.php at the same time. These are:

1) Add new line:
$wgAutopromote['emailconfirmed'] = APCOND_EMAILCONFIRMED;

2) Modify line:
$wgWhitelistRead = array(..., "Speciální:Confirmemail", ... );
to 
$wgWhitelistRead = array(..., "Speciální:Confirmemail", "Speciální:ConfirmEmail", ... );

Unless I do both of these changes at the same time I get the "Nedostatečná oprávnění" (ie. Pemission Error) message. 

Perhaps this experience may help someone else. Regards, Huck.