If your navbar links are not pointing to the correct place, first login to your Admin CP and click on the "vBulletin Options" link in the left frame. Once there, go to the "Site Name / URL / Contact Details" section and verify that your 'Forum URL' option is set correctly (Example: http://vbadvanced.com/forum). There should be no trailing slash or anything like "/index.php" added at the end.
If the first step did not help, click on the "Default Settings" or "Modify Settings" link under the section for your vBadvanced product in the left frame of your Admin CP. One of the first options you will see is called "Navbar Replacements". Ensure that you have the following files listed there, and that you have not mistakenly added your forums URL, or anything else in front of the filenames.
Code:
memberlist.php
usercp.php
register.php
faq.php
calendar.php
search.php
login.php
forumdisplay.php
profile.php
private.php
subscription.php
member.php
online.php
If you have additional links in your navbar which are not listed above, simply add the filename to the list and then save your settings.
If you have a custom style, these links may have been moved to the 'header' template instead. If so, you can copy the filenames listed above and paste them into the 'Header Replacements' option on the same page.