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Well, there are a couple possible issues there: before I list them though, I'd like you to show the output of the following SQL statement:

explain SELECT u.email, u.title, u.url, u.yahoo, u.location, u.use_avatar, u.aim, u.msn, u.signature, u.email_setting, u.num_posts, u.registered, u.admin_note, SUM(r.rep_plus) AS count_rep_plus, SUM(r.rep_minus) AS count_rep_minus, u.reputation_enable, p.id, p.poster AS username, p.poster_id, p.poster_ip, p.poster_email, p.message, p.hide_smilies, p.posted, p.edited, p.edited_by, g.g_id, g.g_user_title, o.user_id AS is_online FROM posts AS p INNER JOIN users AS u ON u.id=p.poster_id INNER JOIN groups AS g ON g.g_id=u.group_id LEFT JOIN online AS o ON (o.user_id=u.id AND o.user_id!=1 AND o.idle=0) LEFT JOIN reputation as r ON (r.user_id=u.id) WHERE p.topic_id=101 GROUP BY p.id ORDER BY p.id LIMIT 2000,25;

That's not nearly enough information to figure out the problem
For one thing, is PunBB the only thing running on the server? If not, then it could very well be something else on the server.
If PunBB is the only possible cause, then you'll need to track down which queries are doing full table scans. If you're using MySQL 5.0, you can log queries that don't use indexes: otherwise you'll have to find some other way (maybe just the normal slow query log with you running the queries through EXPLAIN to find the issue?)

try adding $lang_common to the global bit

Install isn't going to "detect" an old database: its purpose is to install a new copy. Edit the config.php you have so that the details match your old install (I think from your description you just need to change the db_prefix)

My bad then

Not a problem

Lets say you were adding it to the essentials section. You would find the extract elements call it uses, which is

$form = extract_elements(array('timezone', 'language'));

And add the new field to it

$form = extract_elements(array('timezone', 'language', 'email_setting'));

Make sure to remove it from where it currently is as well!

Yes: that doesn't mean the arcade.php you changed to is made for that setup

FIND

$result = $db->query('SELECT COUNT(game_id) FROM '.$db->prefix.'arcade_games') or error('Unable to fetch total game count', __FILE__, __LINE__, $db->error());

REPLACE WITH

$result = $db->query('SELECT COUNT(*) FROM '.$db->prefix.'arcade_games') or error('Unable to fetch total game count', __FILE__, __LINE__, $db->error());

Again though, that script looks like it wasn't written for the current version: it might not work at all

Yes it was: as I noted, I copy/pasted those two lines from your base.css. Only the second line is in an unmodded PunBB.

Compare your Oxygen_cs.css to PunBB's normal Oxygen_cs.css (near the bottom of the file).

First question: the actual update statement is on line 855 of an unmodded profile.php
Second question: Take a look at the switch statement that starts at line 671 in an unmodded PunBB.

Thanks for the report (I've properly closed the tag now).
Please keep in mind, however, that we're not officially accepting bug reports for 1.3 yet.