It's intentional.
Put an empty/default mirc.ini (the one from your appdata dir if you want) into the mIRC exe directory and mIRC will work like it used to pre-6.3.
//copy $qt($mircdirmirc.ini) $qt($nofile($mircexe) $+ mirc.ini)
Note that using the one from your application data dir might keep your application data\ settings like the log directory, script directory, etc. You can use a default one by doing:
//write -c $qt($nofile($mircexe) $+ mirc.ini)
Make sure you restart mIRC for these to work.
Note that in Vista an application cannot write to the Program Files\ directory (by default) so this was partially the reason for the change... it was also done to support multiple user account settings.
