First of all, sorry for bumping this very old thread. I know the topicstarter won't be looking for an answer anymore, but this is the only thread on the web I could find about this topic. All others were about 'omgomg i forgot my root pwd' and 'how do i get the logon screen instead of autologin'. To get the answer to the problem out somewhere findable by Google, I'll reply here.
After about two hours of searching, I finally found out after going through all the files and libraries the PHPMyAdmin index.php included. When your auth_type (see config.inc.php) is set to 'cookie', the file is:
(This was the case in both my local server on my laptop and one I have running 24/7 at home)
Any other auth_type makes it include/require (idk) this file:
(So replace the  by whatever you have as auth_type in the config).
Then, around line 260, the login fields are. I needed this to put in an https warning (not force ssl/https, like possible via the config, only warn). Incase someone else wants to do that too, replace line 259 by:
if( empty($_SERVER["HTTPS"]) )
echo "<h3><font color='darkred'>Waarschuwing: Geen HTTPS verbinding</font></h2>";
(That first } is from another if on line 254: if($GLOBALS['cfg']['AllowArbitraryServer'])
I hope this will be helpfull to someone else on the web (hence the post title), again sorry for the big topic bump. If you do not reply to this, the topic will go down and disappear fastest ;) I would much appreciate if this post and topic would not be deleted, it would have saved me a lot of time.
PS. My PHPMyAdmin version is 3.2.4