Did you change the admincp and modcp directory names in the config.php file also?
Yes, but had the 404 issues when I changed the names in htaccess. So basically right now I have the custom names in config.php, but in htaccess it is the vanilla admincp / modcp names...
And the stuff in the .htaccess is form the DBSEO mod? If it is, perhaps ask Fillip what the trouble may be, as he knows that like the back of his hand.