I've seen that issue with a lot of sites, including this one- if you don't put the 'http' in in your profile for your homepage it goes to
http://www.vbulletin.org/www.yourpage.com - I doubt it's a template issue because if the right code was put in a <a href=""> tag, either would work (with or without the http) - My guess is the parsing code in the php file is messed up, maybe b/c of a mod? I would also check your general settings to make sure your URL's are set right.