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My theory: this happens when there's a bit of lag on the server. This means that when the player goes to login, it's slow, so he refreshes the page a couple times. All the SELECT queries end up getting done before the INSERT, so the online entry is inserted x number of times.
My idea to fix:
1. FIND

            // Update the online list
            if (!$pun_user['logged'])
                $db->query('INSERT INTO '.$db->prefix.'online (user_id, ident, logged) VALUES('.$pun_user['id'].', \''.$db->escape($pun_user['username']).'\', '.$now.')') or error('Unable to insert into online list', __FILE__, __LINE__, $db->error());

REPLACE WITH

            // Update the online list
            if (!$pun_user['logged'])
                $db->query('REPLACE INTO '.$db->prefix.'online (user_id, ident, logged) VALUES('.$pun_user['id'].', \''.$db->escape($pun_user['username']).'\', '.$now.')') or error('Unable to insert into online list', __FILE__, __LINE__, $db->error());

FIND

    // Update online list
    if (!$pun_user['logged'])
        $db->query('INSERT INTO '.$db->prefix.'online (user_id, ident, logged) VALUES(1, \''.$db->escape($remote_addr).'\', '.time().')') or error('Unable to insert into online list', __FILE__, __LINE__, $db->error());

REPLACE WITH

    // Update online list
    if (!$pun_user['logged'])
        $db->query('REPLACE INTO '.$db->prefix.'online (user_id, ident, logged) VALUES(1, \''.$db->escape($remote_addr).'\', '.time().')') or error('Unable to insert into online list', __FILE__, __LINE__, $db->error());

2. Add a compound unique index on user_id and ident.

Basically, this ensures that there will never be more then one online entry for the same user_id and ident.

According to my google search, mod_security can cause that

Arvid: http://www.punres.org/viewtopic.php?id=541 does have that feature afaik

He accidentally deleted the Guest user as well

It's only shown for mods and admins

ultime: It needs more then one query

I'll see what I can do for a plugin (there shouldn't be as many issues as you think).

Edit: mmm, I lied, there's more then just updating posts, there's also topics

You have 2 else's in a row

And when I changed it slightly I got this:

Warning: dl(): Not supported in multithreaded Web servers - use extension statements in your php.ini in c:\apache\htdocs\upload\admin_index.php on line 91

Fatal error: Cannot instantiate non-existent class: win32 in c:\apache\htdocs\upload\admin_index.php on line 92

And enabling that dll file killed Apache when I tried to load the admin index page

Mmm, I really should pay more attention to the address (I didn't realize it was MyPunBB, somehow)
Talk to Connor, like he said in the other thread you must have messed with admin.tpl

You have them confused
Cracker definition

# A cracker is one who engages in one or more of the following: 1) breaks into a computer system; 2) figures out ways to bypass security or license protection in software; 3) intentionally breaches computer security. Contrary to popular belief, Cracker is not synonymous with Hacker.
practice.findlaw.com/glossary.html

# A malicious hacker. Top
www.smoothwall.net/support/glossary.html

You do that anyway for the login table
I can't see a performance hit in doing that