This isn't really the best way to fix this problem, but it worked for me.

First off, my web url is www.officialwla.com/html/

and my situation was that my activation links weren't working in the e-mail's that were getting sent out. (404 not found)

So I changed it from the verification e-mail to the activation link after registration is finished.

When the people would click the activation link on the page, it would give this url
http://officialwla.com/html/officialwla.com/modules.php........

it was adding printing the url twice for some reason.

the way i fixed this was to open the modules/your_account/index.php

I found the variable "$finishlink" which was

$finishlink = "$nukeurl/modules.php?name=$module_name&op=activate&username =$username&check_num=$check_num";

and changed it to

$finishlink = "/html/modules.php?name=$module_name&op=activate&username =$username&check_num=$check_num";

that seemed to fix my problem. If anyone else knows a better way to fix that, please post it!

this quick fix probably is not the best way, but it works for now.